Methods of Treating Cancer with Atovaquone-Related Compounds

ABSTRACT

Described herein are, inter alia, methods for decreasing the growth of a cancer cell, the method comprising delivering to a target cancer cell a growth-inhibitory amount of an atovaquone-related compound, wherein, prior to the delivery, an increased level of activation of the mTOR pathway in the cancer compared to a control level of activation of the mTOR pathway has been found. Also provided are methods for determining the susceptibility of cancer to treatment with an atovaquone-related compound and for assessing the success of therapy with such a compound.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grants R01-CA160979 and F30 CA165740-01 awarded by the National Institutes of Health. The United States government has certain rights in the invention.

TECHNICAL FIELD

This disclosure relates generally to the field of molecular biology and, more particularly, to cancer.

BACKGROUND

The transcription factor, signal transducer and activator of transcription 3 (STAT3), is activated inappropriately in a wide range of human cancers, and drives the malignant behavior of cancer cells. Extensive published evidence indicates that inhibition of STAT3 can have a therapeutic effect on cancer cells, while having minimal toxicity to normal tissue. Further, the mTOR pathway is known to be involved in cancer cell growth and survival (see, e.g., Laplante et al. (2012), su Laplante, M. et al. Cell. 2012 Apr. 13; 149(2): 274-293). Although evidence suggests that inhibiting STAT3 or mTOR would be an effective form of cancer therapy (by itself or in conjunction with chemotherapy, immunotherapy, targeted therapy, and/or radiation therapy), it has been extremely difficult to translate these approaches into the clinic.

SUMMARY

As follows from the Background section above, there is a need in the art for novel compositions and methods of inhibiting STAT3 and/or mTOR for the successful treatment of cancer. It is presently discovered that the compound atovaquone inhibits the STAT3 and mTOR signaling pathways, as well as activates the eIF2α/ATF4 pathway, and can be used to inhibit cancer cell growth and prolong survival and prevent relapse in patients being treated with atovaquone. These and other related benefits are presently provided, and discussed in detail below.

In some aspects, provided herein is a method of decreasing the growth of a cancer cell. The method can include delivering to a target cancer cell a growth-inhibitory amount of an atovaquone-related compound, wherein, prior to the delivery, an increased level of activation of the mammalian target of rapamycin (mTOR) pathway in the cancer compared to a control level of activation of the mTOR pathway has been found. In some aspects of the method, prior to the delivery, an increased level of activation of the signal transducer and activator of transcription 3 (STAT3) pathway in the cancer compared to a control level of activation of the STAT3 pathway has been found. In some aspects of the method, the target cancer cell is in a mammalian subject (e.g., a human subject). In some aspects of the method, the delivery to the target cell can include administration of the atovaquone-related compound to the subject. In some aspects of the method, the level of activation of the mTOR pathway in the cancer was detected in a test sample of or from one or more test cells from the cancer and the control level of activation of the mTOR pathway was detected in a control sample of or from one or more control cells. In some aspects of the method, the level of activation of the mTOR pathway in the cancer was detected in microvesicles or exosomes obtained from a test sample of a body fluid of a subject with the cancer and the control level of activation of the mTOR pathway was detected in a microvesicles or exosomes obtained from a control sample of the body fluid. In some aspects of the method, the level of activation of the STAT3 pathway in the cancer was detected in a test sample of or from one or more test cells from the cancer and the control level of activation of the STAT3 pathway was detected in a control sample of or from one or more control cells. In some aspects of the method, the level of activation of the STAT3 pathway in the cancer was detected in microvesicles or exosomes obtained from a test sample of a body fluid of a subject with the cancer and the control level of activation of the STAT3 pathway was detected in a microvesicles or exosomes obtained from a control sample of the body fluid. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects of the method, the compound is atovaquone and the growth-inhibitory amount of the atovaquone is in a range of about 10 to about 40 mg/kg per day.

In some aspects, the compound is a substituted hydroxynaphthoquinone compound. In some aspects of the above methods, the substituted hydroxynaphthoquinone is a compound of formula (I):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl substituted with aryl, in which aryl is substituted with C₁. In some aspects, R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or n-butyl substituted with decahydronaphthyl. In some aspects, the compound of formula (I) is atovaquone, its isomer, buparvaquone, or TDBHN. In some aspects of the method, the substituted hydroxynaphthoquinone is a compound of formula (II):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl. In some aspects of the method, the compound of formula (II) is parvaquone.

Also provided herein is a method of determining the susceptibility of a cancer in a subject to the growth-inhibitory effect of an atovaquone-related compound. The method can include assessing the level of activation of the mTOR pathway in a test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level activation of the mTOR pathway is not detected in the test sample compared to a control level of activation of the mTOR pathway than if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway. In some aspects of the method, the method further includes assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the STAT3 is detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the STAT3 pathway is not detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway than if an increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample compared to a control level of activation of the mTOR pathway. In some aspects of the method, the test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the test sample includes microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the second test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the second test sample comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the method further includes administering an atovaquone-related compound to the subject if the increased level activation of the mTOR pathway is detected in the test sample. In some aspects of the method, the method further includes administering an atovaquone-related compound to the subject if the increased level of activation of the mTOR pathway is detected in the test sample, if the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample, or if the increased level activation of the mTOR pathway is detected in the test sample and the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample. In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects, the compound is a substituted hydroxynaphthoquinone compound. In some aspects of the above methods, the substituted hydroxynaphthoquinone is a compound of formula (I):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl substituted with aryl, in which aryl is substituted with C₁. In some aspects, R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or n-butyl substituted with decahydronaphthyl. In some aspects, the compound of formula (I) is atovaquone, its isomer, buparvaquone, or TDBHN. In some aspects of the method, the substituted hydroxynaphthoquinone is a compound of formula (II):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl. In some aspects of the method, the compound of formula (II) is parvaquone.

Also provided herein is a method of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound in a subject. The method can include assessing the level of activation of the mTOR pathway in a test sample from a subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is lower than the level of activation of the mTOR pathway in a control sample, and not identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is not lower than the level of activation of the mTOR pathway in a control sample. In some aspects of the method, the method further includes assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is lower than the level of activation of the STAT3 pathway in a control sample or a second control sample, and not identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is not lower than the level of activation of the STAT3 pathway in the control sample or the second control sample. In some aspects of the method, the test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the test sample comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the second test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the second sample comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the control sample or the second control sample was obtained from the subject prior to the treatment with the atovaquone-related compound. In some aspects of the method, the control sample or the second control sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the control sample or second control sample includes microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the subject is a mammalian subject. In some aspects of the method, the mammalian subject is a human subject. In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects, the compound is a substituted hydroxynaphthoquinone compound. In some aspects of the above methods, the substituted hydroxynaphthoquinone is a compound of formula (I):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl substituted with aryl, in which aryl is substituted with C₁. In some aspects, R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or n-butyl substituted with decahydronaphthyl. In some aspects, the compound of formula (I) is atovaquone, its isomer, buparvaquone, or TDBHN. In some aspects of the method, the substituted hydroxynaphthoquinone is a compound of formula (II):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl. In some aspects of the method, the compound of formula (II) is parvaquone.

Also provided herein is a method of treating cancer in a patient. The method can include administering a therapeutically effective amount of an atovaquone-related compound to a patient in need thereof; and, after the administration, monitoring the level of activation of the mTOR pathway in a test sample or two more serial test samples from the patient. In some aspects of the method, the method further includes, after the administration, monitoring the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects of the method, the method further includes continuing the treatment if the level of activation of the mTOR pathway in the test sample or the two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects of the method, the method further includes continuing the treatment if the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects of the method, the test sample or each of the two or more serial test samples is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the test sample or each of the two more serial test samples comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the second test sample or each of the second set of two or more serial test samples comprises a sample of or from one or more cancer cells from the subject. In some aspects of the method, the second test sample or each of the second set of two or more serial test samples can include microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the patient is a mammalian subject. In some aspects of the method, the mammalian subject is a human subject. In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects of the method, the therapeutically effective amount of atovaquone is in a range of about 10 to about 40 mg/kg per day. In some aspects, the compound is a substituted hydroxynaphthoquinone compound. In some aspects of the above methods, the substituted hydroxynaphthoquinone is a compound of formula (I):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl substituted with aryl, in which aryl is substituted with C₁. In some aspects, R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or n-butyl substituted with decahydronaphthyl. In some aspects, the compound of formula (I) is atovaquone, its isomer, buparvaquone, or TDBHN. In some aspects of the method, the substituted hydroxynaphthoquinone is a compound of formula (II):

wherein each of R₁, R₂, R₃, and R₄, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl. In some aspects of the method, the compound of formula (II) is parvaquone. In some aspects of the method, the method can further include administering an additional therapy to the patient. In some aspects of the method, the additional therapy is chemotherapy, immunotherapy, targeted therapy, and/or radiation therapy.

In any of the above-described methods, the level of activation of the mTOR pathway can be determined by detecting the level of phosphorylation of one or more polypeptides selected from the group consisting of mTOR, ribosomal protein S6, S6 kinase, 4E-BP1, eIF2α.

In any of the above-described methods in which the level of activation of the STAT3 pathway is determined, the level of activation of the STAT3 pathway can be determined by detecting the level of one or more of the following markers: STAT3 phosphorylation, nuclear localization of STAT3, STAT3 DNA binding, STAT3-dependent gene expression, and the level of autophosphorylation of JAK family kinases. In some aspects of the method, detecting the level of STAT3 phosphorylation can include determining the level of phosphorylation of tyrosine 705 of human STAT3. In some aspects of the method, detecting STAT3-dependent gene expression comprises determining the expression level of one or more of STAT3 regulated genes encoding polypeptides selected from the group consisting of: myeloid cell leukemia sequence 1 (BCL2-related) (MCL1), jun B proto-oncogene (JUNB), B-cell CLL/lymphoma 6 (BCL6), nuclear factor, interleukin 3 regulated (NFIL3), calpain 2, (m/II) large subunit (CAPN2), early growth response 1 (EGR1), vascular endothelial growth factor A (VEGF), protein tyrosine phosphatase type IVA, member 1 (PTPCAAX1), Kruppel-like factor 4 (KLF4), exostosin glycosyltransferase 1 (EXT1), Niemann-Pick disease, type C1 (NPC1), p21 protein (Cdc42/Rac)-activated kinase 2 (PAK2), pericentrin (PCNT), fibrinogen-like 2 (FGL2), angiopoietin 1 (ANGPT1), GRB10 interacting GYF protein 1 (GIGYF1) (PERQ1), ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6), Brother of CDO (BOC), cysteine dioxygenase (CDO), BCL2-like 1 (BCL2L1) (BCLX), CYCLIN D1, SURVIVIN, and B-cell CLL/lymphoma 2 (BCL2). In some aspects of the method, the level of STAT3 pathway activation correlates with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides selected from the group consisting of MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and BCL2. In some aspects of the method, the level of STAT3 pathway activation correlates inversely with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides selected from the group consisting of PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and CDO.

Also provided herein is a method of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound in a subject. The method can include assessing the level of activation of the eIF2α/ATF4 pathway in a test sample from a subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is increased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample, and not identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is not increased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample. In some aspects of the method, the method further includes determining the level of expression of CHOP and/or CHAC1 and/or REDD1. In some aspects of the method, the method can further include determining the level of mTOR and/or STAT3 activation. In some aspects of the method, the test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the test sample comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the second test sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the second test sample can include microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the control sample or the second control sample was obtained from the subject prior to the treatment with the atovaquone-related compound. In some aspects of the method, the control sample or the second control sample is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the control sample or second control sample can include microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the subject is a mammalian subject (e.g., human subject). In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects, the compound is a substituted hydroxynaphthoquinone compound. In some aspects of the above methods, the substituted hydroxynaphthoquinone is a compound of formula (I):

wherein each of R₁, R2, R3, and R4, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl substituted with aryl, in which aryl is substituted with C₁. In some aspects, R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or n-butyl substituted with decahydronaphthyl. In some aspects, the compound of formula (I) is atovaquone, its isomer, buparvaquone, or TDBHN. In some aspects of the method, the substituted hydroxynaphthoquinone is a compound of formula (II):

wherein each of R₁, R2, R3, and R4, independently, is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl. In some aspects, R₅ is cyclohexyl. In some aspects of the method, the compound of formula (II) is parvaquone.

Also provided herein is a method of treating cancer in a patient. The method can include administering a therapeutically effective amount of an atovaquone-related compound to a patient in need thereof; and, after the administration, monitoring the level of activation of the eIF2α/ATF4 pathway in a test sample or two or more serial test samples from the patient. In some aspects of the method, the method further includes determining the level of expression of CHOP and/or CHAC1 and/or REDD1. In some aspects of the method, the method further includes, after the administration, monitoring the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects of the method, the method further includes, after the administration, monitoring the level of activation of the mTOR pathway in the test sample, the two or more serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects of the method, the method further includes continuing the treatment if the level of activation of the eIF2α/ATF4 pathway in the test sample or the two or more serial test samples is increased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects of the method, the method further includes continuing the treatment if the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects of the method, the method further includes continuing the treatment if the level of activation of the mTOR pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects of the method, the test sample or each of the two or more serial test samples is a sample of or from one or more cancer cells from the subject. In some aspects of the method, the test sample or each of the two more serial test samples comprises microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the second test sample or each of the second set of two or more serial test samples comprises a sample of or from one or more cancer cells from the subject. In some aspects of the method, the second test sample or each of the second set of two or more serial test samples can includes microvesicles or exosomes obtained from a body fluid of the subject. In some aspects of the method, the body fluid can be blood, lymph, urine, cerebrospinal fluid (CSF), ascites, or pleural fluid. In some aspects of the method, the patient is a mammalian subject (e.g., human subject). In some aspects of the method, the compound is atovaquone. In some aspects of the method, the compound is buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN). In some aspects of the method, the therapeutically effective amount of atovaquone is in a range of about 10 to about 40 mg/kg per day. In some aspects of the method, the method further includes administering an additional therapy to the patient. In some aspects of the method, the additional therapy is selected from the group consisting of chemotherapy, immunotherapy, targeted therapy, and/or radiation therapy.

In any of the above-disclosed methods, the cancer can be a hematological tumor such as, e.g., acute myeloid leukemia, chronic myeloid leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma, acute lymphoblastic leukemia, or chronic lymphocytic leukemia.

In any of the above-disclosed methods, the cancer can be a solid tumor selected from the group consisting of breast cancer, melanoma, lung cancer, ovarian cancer, pancreatic cancer, colorectal cancer, prostate cancer, brain cancer, gastroesophageal cancer, and kidney cancer.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains. In case of conflict, the present document, including definitions, will control.

All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. The materials, methods, and examples disclosed herein are illustrative only and not intended to be limiting.

The details of one or more embodiments of the disclosure are set forth in the accompanying drawings and the description below. Preferred methods and materials are described below, although methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present disclosure. Other features, objects, and advantages of the disclosure will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 is an overview of the strategy used to identify drugs that are potential STAT3 inhibitors based on gene expression. The Connectivity Map was queried with the 12-gene STAT3-associated signature (represented by a square grid with a particular shading pattern). Drugs that induced an opposing gene expression pattern (relative to STAT3) were identified as potential STAT3 inhibitors. In this schematic diagram, each grid represents a quantitative gene expression microarray. The darkness of each square represents the amount of expression of each STAT3 signature gene. A drug that causes a grid pattern that is the opposite of the input STAT3-associated gene signature would be a potential STAT3 inhibitor.

FIG. 2 is a graph showing the results from the Connectivity Map analysis, with more negative scores indicating more dissimilarity with respect to the STAT3 signature (i.e., putative inhibitors of STAT3).

FIG. 3 is a graph quantifying the activity of firefly luciferase in STAT3-luc reporter cells that were pre-treated with atovaquone (AQ) at the indicated concentrations for 1 hour, then stimulated with (+) or without (−) IL-6 (interleukin-6; 10 μg/ml) for 5 hours. P-values (*, p<0.05; **, p<0.01; ***, p<0.001) are shown relative to IL-6 stimulation in the presence of vehicle alone.

FIG. 4 is a graph comparing the level of inhibition (expressed as the fraction of control (stimulated vehicle)) of the indicated STATs (STAT3, STAT1, STAT5) or NFkB following treatment of STAT3-luc, STAT1-luc and STAT5-luc reporter cells with the indicated concentrations of atovaquone.

FIG. 5 is a bar graph quantifying the level of phospho-STAT3 (pSTAT3) in STAT3-luc reporter cells pre-treated with atovaquone (20 μM) for 1 hr, and then stimulated with IL-6 (10 μg/ml) for the indicated lengths of time. pSTAT3 levels were normalized to total STAT3 and relative to phospho-STAT3 in the presence of vehicle.

FIG. 6 is an image of a Western blot result for phoshoSTAT3^(Y705) (pSTAT3^(Y705)), total STAT3 (tSTAT3), gp130, and actin, in cell lysates obtained from murine embryonic fibroblasts (MEFs) pre-treated with atovaquone (AQ) (25 μM) for the indicated time periods (“hr”=hour), then stimulated with IL-6 (5 μg/ml) and soluble IL-6 receptor (20 ng/ml) for 15 minutes.

FIG. 7 contains Western blot results for phospho (p) STAT3^(Y705), STAT3^(S727), and total (t) STAT3 in U266, HEL and NA-6 cells treated for 2.5 hours, 6 hours, and 4 hours, respectively, with vehicle or the indicated concentrations of atovaquone (AQ) or 1 μM JAK inhibitor 1.

FIG. 8 is a bar graph quantifying the gene expression levels of the indicated endogenous STAT3 target genes following treatment of U266 cells with vehicle or 15 μM atovaquone (AQ) for 6 hours.

FIG. 9 contains bar graphs quantifying the gene expression levels of the indicated endogenous STAT3 target genes following treatment of INA-6 cells (upper graph) and HEL cells (lower graph) with vehicle or the indicated concentration of atovaquone (AQ) for 6 hours.

FIG. 10 is a line graph comparing cell viability of hematologic cancer cells INA-6, U266, HEL, which have activated STAT3, with non-malignant peripheral blood mononuclear cells (PBMC) (average of donors), following treatment for 72 hours with the indicated concentrations of atovaquone.

FIG. 11 contains fluorescence flow cytometry (FFC) dot plots of INA-6 cells treated for 24 hours with vehicle (left graph) or 15 μM atovaquone (right graph) and stained with propidium iodine (PI) (Y-axis) and Annexin V antibody (X-axis).

FIG. 12 contains FFC dot plots of U226 cells (upper graphs) and HEL cells (lower graphs) treated for 24 hours with vehicle (left graphs) or 15 μM atovaquone (right graphs) and stained with propidium iodine (PI) (Y-axis) and Annexin V antibody (X-axis).

FIG. 13 contains FFC histograms quantifying DNA content (as an indicator of proliferation phase (G1, S and G2/M)) in HEL cells treated for 24 hours with 25 μM atovaquone.

FIG. 14A contains photographs of Western blots for pTyr and pTYK2 following lysis of U266 cells treated with vehicle, atovaquone (15 μM) or JAK inhibitor 1 (1 μM) for 1 hour and immunoprecipitation with TYK2.

FIG. 14B contains photographs of Western blots for pTyr, pJAK2Y570, pJAK2Y1007/1008 and total JAK2 (tJAK2) following lysis of HEL cells treated with atovaquone (20 μM) or JAK inhibitor 1 (1 μM) for 6 hours, followed by immunoprecipitation to JAK2.

FIG. 15 contains a bar graph quantifying kinase activity (expressed as percent of vehicle) for the indicated kinases (JAK1, JAK2, JAK3, TYK2, SRC) determined using in vitro kinase assays (Invitrogen SelectScreen) and following treatment with atovaquone (AQ) (15 μM) or JAK inhibitor 1 (0.5 μM).

FIG. 16 contains FFC histograms plotting levels of cell surface expression of gp130 and IL-6 receptor (IL6R) on U266 cells treated with vehicle, atovaquone (20 μM), JAK inhibitor 1 (1 μM), or Brefeldin A (3 μg/ml) for 2.5 hours.

FIG. 17 contains FFC histograms plotting levels of cell surface expression of gp130 determined by flow cytometry in INA-6 cells (upper panel) or HEL cells (mid and lower panels) treated with vehicle or atovaquone (AQ) ((INA-6 cells: 20 μM AQ, for 4 hours; HEL cells: 25 μM AQ, for 6 or 16 hours)).

FIG. 18 contains photographs of Western blots of lysates of U266 cells treated with vehicle or 20 μM atovaquone (AQ) for the indicated time period (“hr”=hour(s)). Blots were probed for phospho (p) and total (t) STAT3, as well as gp130, and tubulin.

FIG. 19 contains FFC histograms (upper two panels) and photographs of Western blots (lower panel) for gp130 expression (cell surface staining shown in histograms; total protein in Western blot results) in U266 cells treated with vehicle (“Veh”) or atovaquone (AQ) at 20 μM.

FIG. 20 contains photographs of Western blots for the indicated proteins at the indicated time points (6 or 12 hours) following treatment of the indicated cells (MEF, MDA-MB-468, and SKBR3) with vehicle (“Veh) or 25 μM atovaquone (AQ).

FIG. 21 is a bar graph quantifying gp130 mRNA expression in MEF, MDA-MB, SKBR3 and U266 cells treated for 12 hours with vehicle (“Veh) or 25 μM atovaquone (AQ).

FIG. 22 is a line graph comparing the viability (relative to vehicle) of MOLM-13, AML3, SET2, MV-4-11, and MM.1S cells, which are hematologic cancer cell lines that lack STAT3 activation, following treatment for 72 hours with the indicated concentrations (μM) of atovaquone.

FIG. 23 is a line graph comparing the viability (relative to vehicle) of K562, HL60, AML2 and RPMI-8226 cells, which are hematologic cancer cells that lack constitutive STAT3 activation, following treatment for 72 hours with the indicated concentrations (μM) of atovaquone.

FIG. 24 contains FFC dot plots of K562 cells (upper plots) and AML2 cells (lower plots) treated with vehicle or atovaquone (20 μM and 15 μM, respectively), stained for PI and Annexin V and analyzed by flow cytometry.

FIG. 25 contains FFC histograms for PI cell cycle analysis of K562 cells treated with vehicle or atovaquone (20 μM) for 24 hours. Cell cycle phases G1, S and G2/M are indicated.

FIG. 26 contains photographs of Western blots of lysates of K562 cells treated with vehicle (Veh), atovaquone (AQ, 20 μM) or rapamycin (Rapa, 10 μM) for 1 hour or 5 hours, and immunoblotted for phospho (p) and total (t) ribosomal protein S6 (S6), and 4E-BP1.

FIG. 27 contains photographs of Western blots of lysates of K562 cells treated for 6 hours with vehicle or the indicated concentrations of atovaquone(AQ) and immunoblotted for phospho (p) and total (t) ribosomal protein S6 kinase (S6K), S6, ribosomal S6 kinase (RSK), and MAP kinase (MAPK).

FIG. 28 contains photographs of Western blots of lysates of K562 cells pretreated with vehicle or cycloheximide (CHX, 2 μg/ml) for 1 hour, then treated with vehicle or atovaquone (AQ, 20 μM) for 5 hours. The lysates were immunoblotted for phospho (p) and total (t) S6K and S6.

FIG. 29 contains photographs of Western blots of lysates of U266 cells pretreated with vehicle or cycloheximide (CHX, 2 μg/ml) for 1 hour, then treated with vehicle or atovaquone (AQ, 15 μM) for 2.5 hours. The lysates were immunoblotted for phospho (p) and total (t) STAT3 and S6.

FIG. 30 is a schematic diagram depicting the strategy used to identify the factor upregulated by atovaquone that is responsible for mTOR inhibition (“AQ”: atovaquone).

FIG. 31 contains photographs of Western blots of lysates of SKBR3 cells transfected with control (siCtrl) or REDD1 siRNA (siREDD1) for 48 hours, then treated with vehicle (Veh) atovaquone (AQ, 25 μM) for 4 hours. Lysates were immunoblotted for phospho (p) and total (t) S6, as well as REDD1, and tubulin.

FIG. 32 contains photographs of Western blots of lysates of TSC2 null (TSC2−/−) murine embryonic fibroblasts (MEFs), alongside their respective littermate control MEFs (“litter ctrl”), that were treated with atovaquone (25 μM) for 2.5 hours. The lysates were immunoblotted for phospho (p) and total (t) S6.

FIG. 33 contains photographs of Western blots of lysates of REDD1 null (REDD1−/−) murine embryonic fibroblasts (MEFs) alongside their respective littermate control MEFs (“litter ctrl”) that were treated with atovaquone (25 μM) for 2.5 hours. The lysates were immunoblotted for phospho (p) and total (t) S6.

FIG. 34 is a graph quantifying the relative viability of K562 and AML2 cells, which lack STAT3 activation, following treatment for 72 hours with 20 μM atovaquone (AQ) and the indicated concentration of rapamycin, resulting in only a modest viability decrease. P-values (*, p<0.01; **, p<0.0001) are shown for the viability after 72-hour atovaquone treatment relative to 100 μM rapamycin for each cell line.

FIG. 35 contains photographs of Western blots of lysates of U266 cells treated with vehicle (Veh) or 20 μM atovaquone (AQ) for the indicated time period (“hr”=hour(s)). The lysates were immunoblotted for phospho (p) and total (t) eIF2α, as well as for ATF4 and actin.

FIG. 36 contains photographs of Western blots of lysates of K562 cells (upper panel) and SKBR cells (lower panel) treated for the indicated time period (“hr”=hour(s)) with vehicle (Veh) or atovaquone (AQ, 20 μM for K562 cells and 25 μM for SKBR cells) immunoblotted for phospho (p) and total (t) eIF2α, as well as for ATF4 and actin.

FIG. 37 is a bar graph quantifying the fold change in ATF4 gene expression in U266 cells treated with vehicle (veh) or atovaquone (AQ) at 15 μM for 2 hours.

FIG. 38 contains bar graphs quantifying the level of spliced XBP1 in U266, K562, and SKBR3 cells treated, from left to right bar in each graph, with vehicle, atovaquone (20, 20, 25 μM respectively), thapsigargin (1 μM), or tunicamycin (5 μg/ml) for 6 hours.

FIG. 39 contains photographs of Western blots of cleaved and uncleaved ATF6 in SKBR3, K562, U266 cells treated with vehicle (Veh) or atovaquone (“AQ”: 25, 20, and 20 μM, respectively). The last lane is a positive control, consisting of U266 cells treated with 5 mM DTT for 1 hour. Due to the insolubility of ATF6, all of these samples were prepared by boiling in sample buffer.

FIG. 40 contains bar graphs quantifying expression of the indicated unfolded protein response (UPR) target genes, which are downstream of ATF4 and upregulated by atovaquone, in U266, K562, and SKBR3 cells treated, from left to right bar in each graph, with vehicle, atovaquone (20, 20, 25 μM respectively), thapsigargin (1 μM), or tunicamycin (5 μg/ml) for 6 hours.

FIG. 41 contains photographs of Western blots of lysates of U266 cells treated with vehicle (Veh), atovaquone (AQ) or the UPR activators tunicamycin (1) (5 μg/ml), thapsigargin (2) (1 μM), and Brefeldin A (3) (3 μg/ml), or with DTT (4) (5 mM) for 2.5 hours, immunoblotted for phospho (p) and total (t) STAT3.

FIG. 42 contains line graphs plotting relapse-free survival (Y-axis) (left graph) or overall survival (right graph) versus time (days post-transplant, X-axis) in AML patients who had high exposure to atovaquone (“high atovaquone”), or who had low exposure to atovaquone (“low atovaquone”), after hematopoietic stem cell transplant (HSCT). The indicated p-values were determined using the log-rank test.

FIG. 43 contains a dot plot quantifying viability of U266 cancer cells grown for 4 days in serum from patients taking trimethoprim/sulfamethoxazole (TMP/SMX) or atovaquone; the indicated p-value was determined using the two-sample t-test.

FIG. 44 is a bar graph quantifying the STAT3-dependent firefly luciferase activity in STAT3-luc reporter cells pre-treated with the indicated compound at the indicated concentration for 1 hour, then stimulated with IL-6 (10 μg/ml) for 5 hours. Control cells were treated with vehicle with (“veh+IL-6”) or without (“veh untx”) IL-6.

FIG. 45 is a photograph of a Western blot of lysates of U266 cells that were treated with the indicated concentration of drug (buparvaquone or 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydroxy-1,4-naphthoquinone (“Sigma”) or DMSO vehicle control (“Veh”) for 2.5 hours. Blots were immunostained with antibodies for total (t) and phospho (p) STAT3 and total (t) and phospho (p) S6.

FIG. 46A is a line graph quantifying the percent (%) tumor volume over time (days of treatment), and FIG. 46B is a Kaplan-Meier survival curve plotting percent survival over time (days of treatment), in a mouse model of multiple myeloma. After mice had a tumor volume reaching 100 mm³, the mice received the indicated treatment (Vehicle (5% benzyl alcohol in water), Mepron or Atovaquone) by oral gavage.

DETAILED DESCRIPTION Overview

As discussed above, despite the importance of STAT3 in cancer, clinically available therapies to inhibit STAT3 are presently limited. As described herein, the FDA-approved drug atovaquone has been discovered to be a novel STAT3 inhibitor. The present Examples demonstrate that atovaquone induced a gene expression signature that opposed the gene expression signature of STAT3. Further, at concentrations readily achieved in human plasma, atovaquone inhibited STAT3 phosphorylation, transcriptional activity, and STAT3-dependent cancer cell viability. Additionally, it has been discovered that atovaquone activates a branch of the unfolded protein response (UPR) involving the eIF2α/ATF4 pathway, and inhibits mammalian target of rapamycin (mTOR) pathway by inducing DNA-damage-inducible transcript 4 (DDIT4) (also known as Regulated in Development and DNA Damage Responses-1 (REDD1)). REDD1 is causally responsible for inhibition of the mTOR pathway. The mTOR signaling pathway senses and integrates a variety of environmental cues to regulate organismal growth and homeostasis. The pathway regulates many major cellular processes and is implicated in an increasing number of pathological conditions, including cancer. Importantly, higher atovaquone exposure was also discovered herein to be associated with improved disease-free survival in patients who underwent hematopoietic stem cell transplant for hematological malignancies. It has been determined in in vitro studies that the atovaquone-related compounds, buparvaquone and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydroxy-1,4-naphthoquinone (an analog available from Sigma-Aldrich) have similar effects as atovaquone (see, Example 8, below). These results establish atovaquone, as well as other atovaquone-related compounds, as novel STAT3 and mTOR inhibitors and anti-cancer therapeutics. Thus, provided herein are methods of treating cancer with atovaquone-related compounds. Moreover, also provided herein, based on the elucidation of the pathways and responses that are modulated by atovaquone, are novel methods for determining whether a particular cancer is susceptible to treatment with an atovaquone-related compound, as well as methods for monitoring whether such treatments are effective.

DEFINITIONS

As used herein, “atovaquone-related compound” means atovaquone as well as compounds that have the same type activity of atovaquone (i.e., functional analogs of atovaquone), including the ability to inhibit the mammalian target of rapamycin (mTOR) pathway, to inhibit the activated signal transducer and activator of transcription 3 (STAT3) pathway, and to induce activation of the eIF2α/ATF4 pathway. Typically, but not necessarily, atovaquone-related compounds are structural analogs of atovaquone (e.g., buparvaquone and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydroxy-1,4-naphthoquinone). Methods for determining whether mTOR and/or STAT3 pathways are/is inhibited, e.g., in a cancer cell, are known in the art, and described in detail below. Non-limiting examples of atovaquone-related compounds include, e.g., atovaquone, buparvaquone, parvaquone and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN).

As used herein, a cell (in vitro or in vivo) that has an “activated signal transducer and activator of transcription 3 (STAT3) pathway,” means that a cell expresses active STAT3 such that the STAT3 dimerizes and translocates to the nucleus where it acts as a transcription activator. Markers of activated STAT3 pathway (e.g., expression or downregulation of specific genes and/or a specific gene expression profile) are known in the art, and exemplary markers are described in detail, below. As used herein, a cell (in vitro or in vivo) that has an “increased level of activation of the STAT3 pathway,” is one in which STAT3 activation is increased relative to a control (e.g., a cell in which it is known that the STAT3 pathway is not activated).

As used herein, a cell (in vitro or in vivo) that has an “activated mammalian target of rapamycin (mTOR) pathway,” means that the cell expresses mTOR with active kinase and/or phospho-transferase activity.” The mTOR signaling pathways are known in the art, and described, e.g., in Laplante, M. et al. Cell. 2012 Apr. 13; 149(2): 274-293; and Laplante et al. (Oct. 15, 2009 J Cell Sci 122, 3589-3594). As used herein, a cell (in vitro or in vivo) that has an “increased level of activation of the mTOR pathway,” is one in which mTOR activation is increased relative to a control (e.g., a cell in which it is known that the mTOR pathway is not activated).

As used herein, a cell (in vitro or in vivo) that has an “activated eIF2α/ATF4 pathway,” is one in which eIF2α is phosphorylated and ATF4 is expressed. As used herein, a cell (in vitro or in vivo) that has an “increased level of activation of the eIF2α/ATF4 pathway,” has increased levels of phosphorylated eIF2α and increased expression levels of ATF4, relative to a control (e.g., a cell in which it is known that the eIF2α/ATF4 pathway is not activated). The level of expression of REDD1, CHOP and/or CHAC1 can also be increased relative to a control in a cell that has an increased level of activation of the eIF2α/ATF4 pathway.

As used herein “decreasing the growth of a cancer cell” includes inhibiting the proliferation of a cancer cell and/or killing a cancer cell by, for example, the induction of necrosis or of apoptosis of the cancer cell. As used herein, a “growth inhibitory amount,” e.g., of an atovaquone-related compound means an amount of the compound sufficient to decrease the growth of a cancer cell, as defined above. A growth inhibitory amount can be a “therapeutically effective” amount. The terms “therapeutically effective” and “effective amount,” used interchangeable, refer to that quantity of a composition, compound or pharmaceutical formulation that is sufficient to reduce or eliminate at least one symptom of a disease or condition specified herein, e.g., cancer. When a combination of active ingredients is administered, the effective amount of the combination may or may not include amounts of each ingredient that would have been effective if administered individually. The dosage of the therapeutic formulation will vary, depending upon the nature of the disease or condition, the patient's medical history, the frequency of administration, the manner of administration, the clearance of the agent from the host, and the like. The initial dose may be larger, followed by smaller maintenance doses. The dose may be administered, e.g., weekly, biweekly, daily, semi-weekly, etc., to maintain an effective dosage level. Therapeutically effective dosages can be determined stepwise by combinations of approaches such as (i) characterization of effective doses of the composition or compound in in vitro cell culture assays using tumor cell growth and/or survival as a readout followed by (ii) characterization in animal studies using tumor growth inhibition and/or animal survival as a readout, followed by (iii) characterization in human trials using enhanced tumor growth inhibition and/or enhanced cancer survival rates as a readout.

As used herein, “delivering to a target cancer cell” in the context of an atovaquone related compound means causing a cancer cell to come into contact with the compound. In vivo, this can be achieved by various routes of administration, depending on the location of the target cell (e.g., systemic delivery, direct intratumoral delivery, mucosal delivery, etc.). It can also mean conjugating the compound to an agent that specifically targets a cancer cell (e.g., an antibody specific for a cancer cell surface marker). In vitro, delivery of a compound to a target cancer cell can be achieved by adding the compound to the cell culture media, using liposomes, etc. “Delivering to a target cell” can, but does not necessarily, include delivery to the interior of the target cell.

As used herein, a sample that is “of or from one or more cells” (e.g., of or from one or more cancer cells or of or from one or more control cells), means that the sample can be derived from the cell or cells (the sample can be, e.g., a cell lysate, nucleic acid, protein, or other product obtained from and/or prepared from the cells) or can be the cells themselves.

As used herein, a cancer that is “susceptible” to a therapy disclosed herein means that the cancer cell, as a result of exposure to the therapy (e.g., treatment with an atovaquone-related compound), will have decreased growth and/or survival.

As used herein, “prior to treatment” means from any time after cancer develops in the subject to immediately before or at the same time as administration of the first treatment with an atovaquone-related compound.

As used herein, “administering an additional therapy” in the context of administering an atovaquone-related compound means administering the atovaquone-related compound and at least one additional therapy that is not atovaquone. Administering an atovaquone-related compound and an additional therapy is also referred to herein as a “combination therapy.” Additional therapies can include an additional treatment for cancer (e.g., chemotherapy (e.g., administering a chemotherapeutic agent), administering a biologic agent, e.g., antigen, vaccine, antibody etc., administering a cytokine, radiation therapy, immunotherapy, and/or surgery, etc.). Such combination therapy can be sequential therapy wherein the patient is treated first with one therapy and then the other, and so on, or all therapies can be administered simultaneously. In either case, these therapies are said to be coadministered. It is to be understood that “coadministered” does not necessarily mean that the drugs and/or therapies are administered in a combined form (i.e., they may be administered separately or together to the same or different sites at the same or different times).

As used herein, the “expression level” of a gene, such as, e.g., MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, CDO, BCLX, SURVIVIN, BCL2. etc., means the mRNA and/or protein expression level of the gene in a sample (e.g., the level of the polypeptide encoded by the gene can be detected by immunoassay), which can be determined by any suitable method known in the art, such as, but not limited to Northern blot, polymerase chain reaction (PCR), e.g., quantitative real-time, “QPCR”, Western blot, immunoassay (e.g., ELISA), immunohistochemistry, cell immunostaining and fluorescence activated cell sorting (FACS), etc.

As used herein, the term “subject” means any animal, including any vertebrate including any mammal, and, in particular, a human, and can also be referred to, e.g., as an individual or patient. A non-human mammal can be, for example, without limitation a non-human primate (such as a monkey, baboon, gorilla, or orangutan), a bovine animal, a horse, a whale, a dolphin, a sheep, a goat, a pig, a dog, a feline animal (such as a cat), a rabbit, a guinea pig, a hamster, a gerbil, a rat, or a mouse. Non-mammalian vertebrates include without limitation, a bird, a reptile, or a fish.

As used herein, “treating” or “treatment” of a state, disorder or condition includes: (1) preventing or delaying the appearance of clinical or sub-clinical symptoms of the state, disorder or condition developing in a mammal that may be afflicted with or predisposed to the state, disorder or condition but does not yet experience or display clinical or subclinical symptoms of the state, disorder or condition; and/or (2) inhibiting the state, disorder or condition, i.e., arresting, reducing or delaying the development of the disease or a relapse thereof (in case of maintenance treatment) or at least one clinical or sub-clinical symptom thereof; and/or (3) relieving the disease, i.e., causing regression of the state, disorder or condition or at least one of its clinical or sub-clinical symptoms; and/or (4) causing a decrease in the severity of one or more symptoms of the disease. The benefit to a subject to be treated is either statistically significant or at least perceptible to the patient or to the physician.

As used herein, the term “treating cancer” means causing a partial or complete decrease in the rate of growth of a tumor, and/or in the size of the tumor and/or in the rate of local or distant tumor metastasis, and/or the overall tumor burden in a subject, and/or any decrease in tumor survival, in the presence of an inhibitor (e.g., an atovaquone-related compound) described herein.

As used herein, the term “preventing a disease” (e.g., preventing cancer) in a subject means for example, to stop the development of one or more symptoms of a disease in a subject before they occur or are detectable, e.g., by the patient or the patient's doctor. Preferably, the disease (e.g., cancer) does not develop at all, i.e., no symptoms of the disease are detectable. However, it can also result in delaying or slowing of the development of one or more symptoms of the disease. Alternatively, or in addition, it can result in the decreasing of the severity of one or more subsequently developed symptoms.

As used herein, the phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are generally believed to be physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human. As used herein, the term “pharmaceutically acceptable derivative” means any pharmaceutically acceptable salt, solvate or prodrug, e.g., ester, of an atovaquone-related compound described herein, which upon administration to the recipient is capable of providing (directly or indirectly) a compound described herein, or an active metabolite or residue thereof. Such derivatives are recognizable to those skilled in the art, without undue experimentation. Nevertheless, reference is made to the teaching of Burger's Medicinal Chemistry and Drug Discovery, 5th Edition, Vol 1: Principles and Practice, which is incorporated herein by reference to the extent of teaching such derivatives. Pharmaceutically acceptable derivatives include salts, solvates, esters, carbamates, and/or phosphate esters.

The term “nucleic acid hybridization” refers to the pairing of complementary strands of nucleic acids. The mechanism of pairing involves hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases (nucleobases) of the strands of nucleic acids. For example, adenine and thymine are complementary nucleobases that pair through the formation of hydrogen bonds. Hybridization can occur under varying circumstances. Nucleic acid molecules are “hybridizable” to each other when at least one strand of one nucleic acid molecule can form hydrogen bonds with the complementary bases of another nucleic acid molecule under defined stringency conditions. Stringency of hybridization is determined, e.g., by (i) the temperature at which hybridization and/or washing is performed, and (ii) the ionic strength and (iii) concentration of denaturants such as formamide of the hybridization and washing solutions, as well as other parameters. Hybridization requires that the two strands contain substantially complementary sequences. Depending on the stringency of hybridization, however, some degree of mismatches may be tolerated. Under “low stringency” conditions, a greater percentage of mismatches are tolerable (i.e., will not prevent formation of an anti-parallel hybrid). See Molecular Biology of the Cell, Alberts et al., 3rd ed., New York and London: Garland Publ., 1994, Ch. 7.

Typically, hybridization of two strands at high stringency requires that the sequences exhibit a high degree of complementarity over an extended portion of their length. Examples of high stringency conditions include: hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% SDS, 1 mM EDTA at 65° C., followed by washing in 0.1×SSC/0.1% SDS (where 1×SSC is 0.15 M NaCl, 0.15 M Na citrate) at 68° C. or for oligonucleotide (oligo) inhibitors washing in 6×SSC/0.5% sodium pyrophosphate at about 37° C. (for 14 nucleotide-long oligos), at about 48° C. (for about 17 nucleotide-long oligos), at about 55° C. (for 20 nucleotide-long oligos), and at about 60° C. (for 23 nucleotide-long oligos).

Conditions of intermediate or moderate stringency (such as, for example, an aqueous solution of 2×SSC at 65° C.; alternatively, for example, hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% SDS, 1 mM EDTA at 65° C. followed by washing in 0.2×SSC/0.1% SDS at 42° C.) and low stringency (such as, for example, an aqueous solution of 2×SSC at 55° C.), require correspondingly less overall complementarity for hybridization to occur between two sequences. Specific temperature and salt conditions for any given stringency hybridization reaction depend on the concentration of the target DNA or RNA molecule and length and base composition of the probe, and are normally determined empirically in preliminary experiments, which are routine (see Southern, J. Mol. Biol. 1975; 98:503; Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 2, ch. 9.50, CSH Laboratory Press, 1989; Ausubel et al. (eds.), 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & Sons, Inc., New York, at p. 2.10.3). An extensive guide to the hybridization of nucleic acids is found in, e.g., Tijssen (1993) Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes part I, chapt 2, “Overview of principles of hybridization and the strategy of nucleic acid probe assays,” Elsevier, N.Y. (“Tijssen”).

As used herein, the term “standard hybridization conditions” refers to hybridization conditions that allow hybridization of two nucleotide molecules having at least 50% sequence identity. According to a specific embodiment, hybridization conditions of higher stringency may be used to allow hybridization of only sequences having at least 75% sequence identity, at least 80% sequence identity, at least 90% sequence identity, at least 95% sequence identity, or at least 99% sequence identity.

As used herein, the phrase “under hybridization conditions” means under conditions that facilitate specific hybridization of a subset of capture oligonucleotides to complementary sequences present in the cDNA or cRNA. The terms “hybridizing specifically to” and “specific hybridization” and “selectively hybridize to,” as used herein refer to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under at least moderately stringent conditions, and preferably, highly stringent conditions, as discussed above.

“Polypeptide” and “protein” are used interchangeably and mean any peptide-linked chain of amino acids, regardless of length or post-translational modification.

As used herein, the term “nucleic acid” or “oligonucleotide” refers to a deoxyribonucleotide or ribonucleotide in either single- or double-stranded form. The term also encompasses nucleic-acid-like structures with synthetic backbones. DNA backbone analogues provided by the disclosure include phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, phosphoramidate, alkyl phosphotriester, sulfamate, 3′-thioacetal, methylene(methylimino), 3′-N-carbamate, morpholino carbamate, and peptide nucleic acids (PNAs); see Oligonucleotides and Analogues, a Practical Approach, edited by F. Eckstein, IRL Press at Oxford University Press (1991); Antisense Strategies, Annals of the New York Academy of Sciences, Volume 600, Eds. Baserga and Denhardt (NYAS 1992); Milligan (1993) J. Med. Chem. 36:1923-1937; Antisense Research and Applications (1993, CRC Press). PNAs contain non-ionic backbones, such as N-(2-aminoethyl) glycine units. Phosphorothioate linkages are described in WO 97/03211; WO 96/39154; Mata (1997) Toxicol. Appl. Pharmacol. 144:189-197. Other synthetic backbones encompassed by the term include methyl-phosphonate linkages or alternating methylphosphonate and phosphodiester linkages (Strauss-Soukup (1997) Biochemistry 36:8692-8698), and benzylphosphonate linkages (Samstag (1996) Antisense Nucleic Acid Drug Dev 6:153-156). The term nucleic acid is used interchangeably with cDNA, cRNA, mRNA, oligonucleotide, probe and amplification product.

Methods for Measuring the Level of Activation of eIF2α/ATF4, mTOR, and STAT3 Pathways

Methods are provided herein (e.g., for decreasing cancer cell growth, for treating cancer, for determining the susceptibility of a cancer in a subject to the growth-inhibitory effect of atovaquone, for assessing the efficacy of a cancer treatment, etc.) that comprise delivering an atovaquone-related compound to a cancer cell or a subject with cancer, wherein the cell and/or subject has an “increased level of activation of the mTOR pathway” and/or an “increased level of activation of the STAT3 pathway.” In other embodiments, it is desirable to determine whether the level of activation of the mTOR, STAT3 and/or eIF2α/ATF4 pathways has changed (increased or decreased) relative to a control (e.g., a control sample obtained prior to treatment with an atovaquone-related compound). The mTOR, STAT3 and/or eIF2α/ATF4 pathways are known and described in the art. The skilled artisan will appreciate how to determine whether these pathways are activated in a cell and/or subject (e.g., a cancer patient); however, exemplary methods and markers of activation are described below.

In some embodiments, it is desirable to determine (e.g., assay, measure, approximate) the level (e.g., expression or activity), the level of STAT3- and mTOR-regulated genes or any other target gene of interest.

The expression level of the exemplary genes described below can be determined according to any suitable method known in the art. A non-limiting example of such a method includes real-time PCR (RT-PCR), e.g., quantitative RT-PCR (QPCR), which measures the expression level of the mRNA encoding the polypeptide. Real-time PCR evaluates the level of PCR product accumulation during amplification. RNA (or total genomic DNA for detection of germline mutations) is isolated from a sample. RT-PCR can be performed, for example, using a Perkin Elmer/Applied Biosystems (Foster City, Calif.) 7700 Prism instrument. Matching primers and fluorescent probes can be designed for genes of interest using, based on the genes' nucleic acid sequences (e.g., as described above), for example, the primer express program provided by Perkin Elmer/Applied Biosystems (Foster City, Calif.). Optimal concentrations of primers and probes can be initially determined by those of ordinary skill in the art, and control (for example, beta-actin) primers and probes may be obtained commercially from, for example, Perkin Elmer/Applied Biosystems (Foster City, Calif.).

To quantitate the amount of the specific nucleic acid of interest in a sample, a standard curve is generated using a control. Standard curves may be generated using the Ct values determined in the real-time PCR, which are related to the initial concentration of the nucleic acid of interest used in the assay. Standard dilutions ranging from 10-106 copies of the gene of interest are generally sufficient. In addition, a standard curve is generated for the control sequence. This permits standardization of initial content of the nucleic acid of interest in a tissue sample to the amount of control for comparison purposes. Methods of QPCR using TaqMan probes are well known in the art. Detailed protocols for QPCR are provided, for example, for RNA in: Gibson et al., 1996, Genome Res., 10:995-1001; and for DNA in: Heid et al., 1996, Genome Res., 10:986-994; and in Innis et al. (1990) Academic Press, Inc. N.Y.

Expression of mRNA, as well as expression of peptides and other biological factors, can also be determined using microarray, methods for which are well known in the art [see, e.g., Watson et al. Curr Opin Biotechnol (1998) 9: 609-14; “DNA microarray technology: Devices, Systems, and Applications” Annual Review of Biomedical Engineering; Vol. 4: 129-153 (2002); Chehab et al. (1989) “Detection of specific DNA sequences by fluorescence amplification: a color complementation assay” Proc. Natl. Acad. Sci. USA, 86: 9178-9182; Lockhart et al. (1996) “Expression monitoring by hybridization to high-density oligonucleotide arrays” Nature Biotechnology, 14: 1675-1680; and M. Schena et al. (1996) “Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes” Proc. Natl. Acad. Sci. USA, 93:10614-10619; Peptide Microarrays Methods and Protocols; Methods in Molecular Biology; Volume 570, 2009, Humana Press; and Small Molecule Microarrays Methods and Protocols; Series: Methods in Molecular Biology, Vol. 669, Uttamchandani, Mahesh; Yao, Shao Q. (Eds.) 2010, 2010, Humana Press]. For example, mRNA expression profiling can be performed to identify differentially expressed genes, wherein the raw intensities determined by microarray are log 2-transformed and quantile normalized and gene set enrichment analysis (GSEA) is performed according, e.g., to Subramanian et al. (2005) Proc Natl Acad Sci USA 102:15545-15550).

Other suitable amplification methods include, but are not limited to, ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4:560, Landegren et al. (1988) Science 241:1077, and Barringer et al. (1990) Gene 89:117), transcription amplification (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173), self-sustained sequence replication (Guatelli et al. (1990) Proc. Nat. Acad. Sci. USA 87:1874), dot PCR, and linker adapter PCR, etc.

Methods for determining DNA binding, e.g., STAT3 binding to DNA in the nucleus, are known in the art, and include, e.g., measured binding in vivo by chromatin immunoprecipitation (ChIP), and measured in vitro by electrophoretic mobility shift assay (EMSA). For example, for EMSA, the LightShift EMSA Kit (Pierce) can be used according to the manufacturer's protocol. STAT binding reactions can be performed as described (e.g., in Battle T E & Frank D A (2003) STAT1 mediates differentiation of chronic lymphocytic leukemia cells in response to Bryostatin 1. Blood 102(8):3016-3024) using 5′-biotinylated 25 bp probes. The ChIP method is described, e.g., in Nelson E A, et al. Identification of unique STAT5 targets by chromatin immunoprecipitation-based gene identification. J. Biol. Chem. 2004; 279:54724-54730.

Other methods for detecting gene expression (e.g., mRNA levels) include Serial Analysis of Gene Expression applied to high-throughput sequencing (SAGEseq), as described in Wu Z J et al. Genome Res. 2010 December; 20(12):1730-9. 2.

Methods for detecting the expression levels of polypeptides are also known in the art. Non-limiting examples of suitable methods for detecting expression levels of gene products (i.e., polypeptides) described herein include, e.g., flow cytometry, immunoprecipitation, Western blot (see, e.g., Battle T E, Arbiser J, & Frank D A (2005) The natural product honokiol induces caspase-dependent apoptosis in B-cell chronic lymphocytic leukemia (B-CLL) cells. Blood 106(2):690-697), ELISA (enzyme-linked immunosorbent assay) and/or immunohistochemistry.

eIF2α/ATF4 Pathway

It is presently discovered that atovaquone-related compounds activate certain components of the unfolded protein response (UPR). In particular, it was demonstrated in the present Examples that atovaquone induced Eukaryotic Initiation Factor 2 alpha (eIF2α) phosphorylation and expression of Activating transcription factor 4 (tax-responsive enhancer element B67) (ATF4) (i.e., the EFIα/ATF4 pathway), but not other branches of the UPR. Moreover, expression of CCAAT/-enhancer-binding protein homologous protein (CHOP), cation transport regulator-like protein 1 (CHAC1) and Regulated in Development and DNA Damage Responses-1 (REDD1) were increased following activation of the pathway.

While broad UPR activation has variable effects in cancer, the EFIα/ATF4 pathway has been shown to promote apoptosis in numerous cancer contexts (see, e.g., Little J L, et al. (2007) Inhibition of fatty acid synthase induces endoplasmic reticulum stress in tumor cells. Cancer Research 67(3):1262-1269; Liu G, et al. (2012) Salermide up-regulates death receptor 5 expression through the ATF4-ATF3-CHOP axis and leads to apoptosis in human cancer cells. Journal of Cellular and Molecular Medicine 16(7):1618-1628; Oyadomari S & Mori M (2004) Roles of CHOP/GADD153 in endoplasmic reticulum stress. Cell Death and Differentiation 11(4):381-389; Rao R, et al. (2010) Treatment with panobinostat induces glucose-regulated protein 78 acetylation and endoplasmic reticulum stress in breast cancer cells. Molecular Cancer Therapeutics 9(4):942-952; and Sanchez A M, et al. (2008) Induction of the endoplasmic reticulum stress protein GADD153/CHOP by capsaicin in prostate PC-3 cells: a microarray study. Biochemical and Biophysical Research Communications 372(4):785-791). Atovaquone strongly upregulates CHOP with no effect on levels of BiP, supporting the role of the EFIα/ATF4 pathway in atovaquone-mediated apoptosis. CHAC1, an EFIα/ATF4 target gene consistently upregulated by atovaquone, is also pro-apoptotic (Mungrue Ind., et al. (2009) CHAC1/MGC4504 is a novel proapoptotic component of the unfolded protein response, downstream of the ATF4-ATF3-CHOP cascade. J Immunol 182(1):466-476). Thus, atovaquone inhibits the viability of cancer cells through STAT3-related and STAT3-independent mechanisms.

Thus, in certain aspects, effective inhibition of tumor growth and/or treatment of cancer using an atovaquone-related compound can be determined/monitored by determining whether the levels of eIF2α phosphorylation and/or ATF4 (i.e., the eIF2α/ATF4 pathway) are increased, decreased, or not increased or not decreased, relative to a control.

Thus, in some embodiments, methods of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound in a subject are provided, wherein the method comprises: (a) assessing the level of activation of the eIF2α/ATF4 pathway in a test sample from a subject that has been treated with the compound, (b) identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is increased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample, and (c) not identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is not increased and/or decreased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample. In some embodiments, the method further comprises determining the level of expression of CHOP, CHAC1 and/or REDD1, wherein increased expression of one or both of the genes or the polypeptides encoded by these genes correlates with activation of the eIF2α/ATF4 pathway. CHAC1 is a target gene of CHOP (see, Mungrue Ind., Pagnon J, Kohannim O, Gargalovic P S, & Lusis A J (2009) CHAC1/MGC4504 is a novel proapoptotic component of the unfolded protein response, downstream of the ATF4-ATF3-CHOP cascade. J Immunol 182(1):466-476). In some aspects, the method comprises determining the level of phosphorylation of eIF2α, wherein its increased phosphorylation correlates with activation of the eIF2α/ATF4 pathway. In other aspects, the method comprises determining the expression level of ATF4, wherein increased expression of ATF4 gene or the polypeptide encoded by ATF4 correlates with activation of the eIF2α/ATF4 pathway.

The level of activation or any relative change (e.g., compared to a prior measurement) in the level of activation of the eIF2α/ATF4 pathway in a cell (e.g., a cancer cell) can be determined by detecting, for example, the expression level of one or more of the genes involved in the eIF2α/ATF4 pathway, such as, but not limited to, the genes encoding REDD1, DNA-damage-inducible transcript 3 (DDIT3) (also known as CHOP), activating transcription factor 3 (ATF3), cation transport regulator homolog 1 (CHAC1), and activating transcription factor 4 (ATF4).

The expression levels of these genes can be determined by any suitable method known in the art. For example, the nucleic and amino acid sequences for these genes are known and can be used to determine whether the genes are expressed. By way of non-limiting example, the GenBank® Accession numbers for the human nucleic acid sequences of these genes, as well as the human amino acid sequences encoded by those genes are set forth in Table 1, below:

TABLE 1 GenBank ® Accession Nos. Nucleic Acid SEQ ID Amino Acid SEQ Gene Name GenBank ® No. NO. GenBank ® No. ID NO. REDD1 NM_019058 1 NP_061931 2 CHOP NM_001195053 3 NP_001181982 4 ATF3 NM_001030287 5 NP_001025458 6 CHAC1 BC019625 7 AAH19625.1 8 ATF4 NM_001675 9 NP_001666 10

Phosphorylation of eIF2α can be determined by any method known in the art. For example, Western blot, using an antibody specific for the phosphorylated form of eIF2α can be used. Expression levels of CHOP, CHAC1, ATF4 and REDD1 can be determined using Q-PCR for measuring gene expression, and by ELISA for measuring protein expression. Methods for designing primers for Q-PCR, based on the known nucleic acid sequences of these proteins (see, e.g., Table 1, above), are known in the art. Antibodies for detecting, e.g., by ELISA, Western blot, flow cytometry, and/or immunohistochemistry, are commercially available. For example, REDD1 antibody is available from Proteintech, antibody recognizing eIF2α (total and phosphorylated form) are available from Cell Signaling Technology, antibody recognizing full-length and cleaved ATF6 is available from Abcam, CHOP-specific antibodies are available, e.g., from Thermo Scientific (Pierce Antibody) (Rockford, Ill.).

mTOR Pathway

It is presently discovered that atovaquone-related compounds are potent inhibitors of the mTOR signaling pathway, or “mTOR pathway.” The mTOR pathway is known to be involved in cancer cell growth and survival (see, e.g., the comprehensive review by Laplante et al. (2012), supra). The mTOR protein is a 289-kDa serine-threonine kinase that belongs to the phospho-inositide 3-kinase (PI3K)-related kinase family and is conserved throughout evolution. mTOR nucleates at least two distinct multi-protein complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2).

The nucleic acid and amino acid sequences for human mTOR are known and have the following GenBank® Accession Nos.: NM_004958 (mRNA) (SEQ ID NO: 11) and NP_004949 (amino acid) (SEQ ID NO: 12).

In some aspects, the methods disclosed herein encompass determining whether the mTOR pathway is activated in a cell and/or whether its level of activation is increased, decreased, or not increased or not decreased (relative to a control). The mTOR pathway has been extensively studied for decades, and there is a large body of literature describing the many components of the mTOR pathway. Thus, the skilled artisan will understand how to determine whether an mTOR pathway is activated and/or whether its level of activation is increased, decreased, or not increased, or not decreased (e.g., relative to a control), e.g., by looking for presence of one or more known markers of the activated pathway. While these markers are well known in the art, a brief review is provided, below.

Protein synthesis is the best characterized process controlled by mTORC1. mTORC1 directly phosphorylates the translational regulators eukaryotic translation initiation factor 4E (eIF4E) binding protein 1 (4E-BP1) and S6 kinase 1 (S6K1), which, in turn, promote protein synthesis. The phosphorylation of 4E-BP1 prevents its binding to the cap-binding protein eIF4E, enabling it to participate in the formation of the eIF4F complex which is required for the initiation of cap-dependent translation. The activation of S6K1 leads, through a variety of effectors, to an increase in mRNA biogenesis, as well as translational initiation and elongation. S6K1 was originally thought to control the translation of an abundant subclass of mRNAs characterized by an oligopyrimidine tract at the 5′ end (5′ TOP mRNAs) and which encode most of the protein components of the translational machinery. Although mTOR itself is key for the translational control of 5′TOP mRNAs, S6K1 and its substrate ribosomal protein S6 are not required for this process and so how mTORC1 controls the translation of these mRNAs remains unknown.

mTORC1 also upregulates the protein synthesis machinery in other ways: (1) it activates the regulatory element tripartite motif-containing protein-24 (TIF-1A), which promotes its interaction with RNA Polymerase I (Pol I) and the expression of ribosomal RNA (rRNA); and (2) mTORC1 phosphorylates and inhibits Mafl, a Pol III repressor, and so induces 5S rRNA and transfer RNA (tRNA) transcription. The overall role of mTORC1 in the regulation of mRNA translation is highly significant because specific, active-site inhibitors of mTOR that completely inhibit mTORC1 function, significantly reduce overall rates of protein synthesis in proliferating cells in culture.

In addition to regulating the production of proteins, mTORC1 also controls the synthesis of lipids required for proliferating cells to generate membranes. To a large extent, mTORC1 acts through the sterol regulatory element binding protein 1/2 (SREBP1/2) transcription factors that control the expression of numerous genes involved in fatty acid and cholesterol synthesis. The inactive SREBPs reside on the endoplasmic reticulum (ER) and their proteolytic processing in response to insulin or sterol depletion releases an active form that travels to the nucleus to activate transcription. mTORC1 inhibition reduces SREBP1/2 levels as well as processing and markedly lowers the expression of lipogenic genes. mTORC1 appears to regulate SREBP function through several mechanisms, including, at least in some cell types, through S6K1. In addition, mTORC1 phosphorylates Lipin-1, preventing it from entering the nucleus and suppressing SREBP1/2 function and levels. mTORC1 also promotes the expression and activity of peroxisome proliferator-activated receptor γ (PPAR-γ), the master regulator of adipogenesis. mTORC1 also positively regulates cellular metabolism and ATP production.

mTORC1 increases glycolytic flux by activating the transcription and the translation of hypoxia inducible factor 1α (HIF1α), a positive regulator of many glycolytic genes. mTORC1 also increases mitochondrial DNA content and the expression of genes involved in oxidative metabolism, in part, it is thought, by mediating the nuclear association between PPAR-γ coactivator 1α (PGC1α) and the transcription factor Ying-Yang 1 (YY1), which positively regulate mitochondrial biogenesis and oxidative function.

mTORC1 also promotes growth by negatively regulating autophagy, the central degradative process in cells. Autophagy is required for the recycling of damaged organelles and for the organismal and cellular adaptation to nutrient starvation. Upon mTORC1 inhibition, autophagosomes form which then engulf cytoplasmic proteins and organelles and fuse with lysosomes, leading to the degradation of cell components and the recycling of cellular building blocks. In mammals, mTORC1 directly phosphorylates and suppresses ULK1/Atg13/FIP200 (unc-51-like kinase 1/mammalian autophagy-related gene 13/focal adhesion kinase family-interacting protein of 200 kDa), a kinase complex required to initiate autophagy. As with the control of protein and lipid synthesis, mTORC1 is likely to impact autophagy through several mechanisms. For example, mTORC1 regulates death associated protein 1 (DAP1), a suppressor of autophagy and, in a recent analysis of the mTOR-dependent phosphoproteome, WIPI2, a mammalian ortholog of Atg18—a regulator of early autophagosome formation in yeast—emerged as a potential mTOR effector.

mTORC2 controls several members of the AGC subfamily of kinases including Akt, serum- and glucocorticoid-induced protein kinase 1 (SGK1), and protein kinase C-α (PKC-α). Akt regulates cellular processes such as metabolism, survival, apoptosis, growth, and proliferation through the phosphorylation of several effectors. mTORC2 directly activates Akt by phosphorylating its hydrophobic motif (Ser473), a site required for its maximal activation. Defective Akt-Ser473 phosphorylation associated with mTORC2 depletion impairs the phosphorylation of some Akt targets, including forkhead box O1/3a (FoxO1/3a), while other Akt targets like TSC2 and GSK3-β remain unaffected. The fact that Akt activity is not completely abolished in cells lacking mTORC2 likely explains these results. mTORC2 also directly activates SGK1, a kinase controlling ion transport and growth. In contrast to Akt, SGK-1 activity is completely blocked by the loss of mTORC2. Because SGK1 controls FoxO1/3a phosphorylation on residues also phosphorylated by Akt, loss of SGK1 activity is probably responsible for the reduction in FoxO1/3a phosphorylation in mTORC2-depleted cells. PKC-α is the third AGC kinase activated by mTORC2. Along with other effectors such as paxilin and Rho GTPases, the activation of PKC-α by mTORC2 regulates cell shape in cell type-specific fashion by affecting the actin cytoskeleton.

Several observations support the importance of mTOR pathway in cancer pathogenesis. Many components of the PI3K signaling pathway, which is upstream of both mTORC1 and mTORC2, are mutated in human cancers. Additionally, the loss of p53, a very common event in cancer, promotes mTORC1 activation. In addition, several familial cancer syndromes arise from mutations in genes encoding proteins that lie upstream of the mTOR complexes, including Tsc1/2, serine threonine kinase 11 (Lkb1), Pten, and neurofibromatosis type 1 (Nf1). Oncogenic activation of mTOR signaling induces several processes required for cancer cell growth, survival, and proliferation.

In certain embodiments, the methods described herein encompass assessing the level of and/or relative changes in the level of activation of the mTOR pathway (e.g., in a test sample, e.g. of or from a cancer cell). Non-limiting examples of cancers in which the level of mTOR pathway activation is known to be increased include, e.g., endometrial, renal cell, prostate, non-small cell lung, neuroendocrine cancers, as well as glioblastoma multiforme, multiple myeloma, non-Hodgkin lymphoma, chronic myelogenous leukemia, chronic lymphocytic leukemia, acute lymphoblastic leukemia, and acute myeloid leukemia. The skilled artisan will appreciate that the level of mTOR pathway is also increased in other cancers not listed herein; however, such cancers are also encompassed by the present disclosure.

In some embodiments, the level of activation and/or any relative change (e.g., compared to a prior measurement) in the level of activation of the mTOR pathway can be determined by detecting, for example, the level of phosphorylation of one or more polypeptides mTOR, ribosomal protein S6 (S6), S6 kinase (S6K), 4E-BP1, and eIF2α. Further, mTOR is known to phosphorylate STAT3 on serine 727 and increase its transcriptional activity [see, e.g., Yokogami K, et al. (2000) Serine phosphorylation and maximal activation of STAT3 during CNTF signaling is mediated by the rapamycin target mTOR. Current Biology: CB 10(1):47-50]. Thus, phosphoSTAT3 (pSTAT3) is also a marker of activated mTOR pathway.

Methods for measuring the expression levels of phosphorylated polypeptides are known in the art. For example, Western blotting using antibodies specific for phosphorylated forms, as well as non-phosphorylated forms, or total polypeptide (phosphorylated and non-phosphorylated), are commercially available. The presence and/or levels of phosphorylated polypeptides can be compared to the total levels of the polypeptide. Exemplary, non-limiting examples of commercially-available antibodies for detecting markers of activated mTOR pathway are listed in Table 2, below:

TABLE 2 Antibodies for Detecting Total (t) and Phosphorylated (p) Forms of Markers of Activated mTOR Pathway Polypeptide Commercially Available Antibody - Catalog # t-mTOR Cell Signaling Technology - 2972 p-mTOR Cell Signaling Technology - 2976 t-S6 Cell Signaling Technology - 2217 p-S6 Cell Signaling Technology - 2215 t-S6K Cell Signaling Technology - 2708 p-S6K Cell Signaling Technology - 9234 t-4E-BP1 Cell Signaling Technology - 9451 P-4E-BP1 Cell Signaling Technology - 9452 t-eIF2α Cell Signaling Technology - 5324 p-eIF2α Cell Signaling Technology - 9721 t-STAT3 Santa Cruz Biotechnology - sc-7179 phospho-Y705 Cell Signaling Technology - 9131 STAT3 See, also, Frank DA, Mahajan S, & Ritz J (1997) B lymphocytes from patients with chronic lymphocytic leukemia contain signal transducer and activator of transcription (STAT) 1 and STAT3 constitutively phosphorylated on serine residues. The Journal of Clinical Investigation 100(12): 3140-3148. Table legend: “t” in column 1 = total; “p” in column 1 = phospho

STAT3 Pathway

It is presently discovered that atovaquone-related compounds are potent inhibitors of signal transducer and activator of transcription 3 (STAT3). While not intending to bound by theory or any particular mechanism of action, it is demonstrated herein that atovaquone is not a kinase inhibitor, but instead downregulates cell-surface gp130 expression, which is required for STAT3 activation in multiple contexts. An abundance of evidence establishes STAT3 as a central oncogenic mediator. STAT3 activation is transient and tightly-controlled in normal cells, but is often constitutively activated in numerous tumor types to drive target genes regulating growth, survival, invasion, and angiogenesis. A major source of STAT3 activation in malignancy is the cytokine IL-6 (interleukin-6), which signals through a complex of IL-6Rα (interleukin-6 receptor a) and gp130 to activate Janus kinases (JAKs) and induce phosphorylation of STAT3. The importance of IL-6-driven STAT3 activation has been demonstrated in multiple tumor types, including breast, lung, liver, prostate, pancreatic, colon, head and neck, multiple myeloma, and melanoma. The source of IL-6 can be paracrine—derived from non-neoplastic stromal or inflammatory cells—or autocrine, produced by tumor cells.

STAT3 is activated by a plethora of oncogenic kinases and growth factors, and it is specifically required for transformation by v-Src and mutant c-Kit. Conversely, loss of STAT3 inhibits tumor formation in multiple cell types (see, Frank D A (2007) STAT3 as a central mediator of neoplastic cellular transformation. Cancer letters 251(2):199-210)). Moreover, a constitutively-active variant of STAT3, termed STAT3C, is sufficient for neoplastic transformation and induces tumorigenic target genes such as cyclin D1, Bcl-X, and c-Myc (38). STAT3C has cysteine residues introduced near the C-terminus that form intermolecular disulfide bridges, promoting dimerization and transcriptional activity. In addition to transformation and tumor initiation, STAT3 is also critical to tumor maintenance and progression. For example, inhibition of constitutively-active STAT3 in multiple tumor models and cancer cell lines leads to apoptosis (see, Devarajan E & Huang S (2009) STAT3 as a central regulator of tumor metastases. Current Molecular Medicine 9(5):626-633).

STAT3 has numerous targets, and knowledge of how STAT3 acts on these targets can be taken advantage of to determine whether or not the STAT3 pathway is activated (e.g., in a cell, e.g., a cancer cell, e.g., in a cancer patient). The activity of STAT3 and markers of STAT3 activation are known in the art; non-limiting examples are described for various cancers below.

For example, the effects of STAT3 are mediated by the direct regulation of diverse target genes involving all of the hallmarks of cancer (see, Hanahan D & Weinberg R A (2011) Hallmarks of cancer: the next generation. Cell 144(5):646-674). Also, the significance of STAT3 in tumor-stromal interactions is increasingly gaining attention. Uncontrolled proliferation, one of the first cancer hallmarks to be recognized, is advanced by STAT3 at many levels. STAT3 induces cyclin D1 (see, Bromberg J F, et al. (1999) Stat3 as an oncogene. Cell 98(3):295-303; and Sinibaldi D, et al. (2000) Induction of p21WAF1/CIP1 and cyclin D1 expression by the Src oncoprotein in mouse fibroblasts: role of activated STAT3 signaling. Oncogene 19(48):5419-5427), which is critical for G1/S phase transition, as well as cyclins D2/D3/A and the phosphatase cdc25A (see, Fukada T, et al. (1998) STAT3 orchestrates contradictory signals in cytokine-induced G1 to S cell-cycle transition. The EMBO journal 17(22):6670-6677). Moreover, genome-wide profiling of STAT3-regulated genes identified Egr1 and JunB as further targets promoting cell cycle entry (see, e.g., Frank D A (2007) STAT3 as a central mediator of neoplastic cellular transformation. Cancer Letters 251(2):199-210). Also, STAT3 antagonizes the cell cycle inhibitors p21 and p27 by direct transcriptional repression (Fukada et al., supra) and by upregulating Skp2, which mediates their ubiquitin-mediated degradation (see, Huang H, Zhao W, & Yang D (2012) Stat3 induces oncogenic Skp2 expression in human cervical carcinoma cells. Biochemical and biophysical research communications 418(1):186-190).

STAT3 induction of c-Myc, a pleiotropic protein with key roles in cancer growth and proliferation, is required for v-Src transformation and PDGFR-induced mitogenesis (Bowman T, et al. (2001) Stat3-mediated Myc expression is required for Src transformation and PDGF-induced mitogenesis. Proceedings of the National Academy of Sciences of the United States of America 98(13):7319-7324). Moreover, the kinases Pim-1 and Pim-2 are STAT3 targets, and ectopic expression of Pim-1 with c-Myc fully rescues loss of cell cycle progression after STAT3 inhibition (Shirogane T, et al. (1999) Synergistic roles for Pim-1 and c-Myc in STAT3-mediated cell cycle progression and antiapoptosis. Immunity 11(6):709-719). Finally, STAT3 fosters limitless replicative potential by directly inducing telomerase (Konnikova L, Simeone M C, Kruger M M, Kotecki M, & Cochran B H (2005) Signal transducer and activator of transcription 3 (STAT3) regulates human telomerase reverse transcriptase (hTERT) expression in human cancer and primary cells. Cancer Research 65(15):6516-6520).

STAT3 also enhances cancer cell survival. While STAT3 regulates Bcl-2 and mediates chemotherapy resistance, STAT3 regulation of Bcl-X has been better studied. STAT3 is required for Bcl-X expression by EGFR in head and neck squamous cell carcinoma (HNSCC), HER2 in breast cancer, and IL-6 in multiple myeloma (see, Grandis J R, et al. (2000) Constitutive activation of Stat3 signaling abrogates apoptosis in squamous cell carcinogenesis in vivo. Proceedings of the National Academy of Sciences of the United States of America 97(8):4227-4232; Karni R, Jove R, & Levitzki A (1999) Inhibition of pp60c-Src reduces Bcl-XL expression and reverses the transformed phenotype of cells overexpressing EGF and HER-2 receptors. Oncogene 18(33):4654-4662; Catlett-Falcone R, et al. (1999) Constitutive activation of Stat3 signaling confers resistance to apoptosis in human U266 myeloma cells. Immunity 10(1):105-115; and Bowman T, et al. (2000) STATs in oncogenesis. Oncogene 19(21):2474-2488). Mcl-1, a related STAT3 target, collaborates with Bcl-X to resist Fas-mediated cell death, particularly in hematological cancers (Catlett-Falcone R, et al., supra, Epling-Burnette P K, et al. (2001) Inhibition of STAT3 signaling leads to apoptosis of leukemic large granular lymphocytes and decreased Mcl-1 expression. The Journal of Clinical Investigation 107(3):351-362; and Puthier D, et al. (1999) IL-6 up-regulates mcl-1 in human myeloma cells through JAK/STAT rather than ras/MAP kinase pathway. European Journal of Immunology 29(12):3945-3950).

Survivin is another anti-apoptotic protein induced by STAT3 in various settings, including astrocytoma, breast cancer, gastric cancer, and primary effusion lymphoma (see, e.g., Konnikova L, et al. (2003) Knockdown of STAT3 expression by RNAi induces apoptosis in astrocytoma cells. BMC Cancer 3:23; Gritsko T, et al. (2006)). Persistent activation of stat3 signaling induces survivin gene expression and confers resistance to apoptosis in human breast cancer cells. Clinical Cancer Research: an Official Journal of the American Association for Cancer Research 12(1):11-19; Kanda N, et al. (2004) STAT3 is constitutively activated and supports cell survival in association with survivin expression in gastric cancer cells. Oncogene 23(28):4921-4929; and Aoki Y, Feldman G M, & Tosato G (2003) Inhibition of STAT3 signaling induces apoptosis and decreases survivin expression in primary effusion lymphoma. Blood 101(4):1535-1542). Inhibiting STAT3 reduces levels of these survival factors and causes apoptosis, which is reversed by their enforced expression, demonstrating the importance of these downstream effectors (see, Bowman T et al., supra, Gritsko T, et al., supra, Aoki Y. et al., supra, and Lim C P & Cao X (2006) Structure, function, and regulation of STAT proteins. Molecular BioSystems 2(11):536-550).

Additionally, STAT3 transcriptional repression of pro-apoptotic Fas, TNF-α, and p53 facilitates tumor escape from normal death signals (see, Niu G, et al. (2005) Role of Stat3 in regulating p53 expression and function. Molecular and Cellular Biology 25(17):7432-7440, Ivanov V N, et al. (2001) Cooperation between STAT3 and c-jun suppresses Fas transcription. Molecular cell 7(3):517-528; and Niu G, et al. (2001) Overexpression of a dominant-negative signal transducer and activator of transcription 3 variant in tumor cells leads to production of soluble factors that induce apoptosis and cell cycle arrest. Cancer Research 61(8):3276-3280). Self-renewal and resistance to apoptosis are traits of cancer stem cells (CSC), and not surprisingly, STAT3 has been linked to the CSC phenotype. In fact, LIF activation of STAT3 is critical to pluripotency in embryonic stem cells. The STAT3 target genes KLF4 and BCL6 inhibit differentiation (see, Frank et al., supra), while another STAT3 target, DNA methyltransferase I (see, Zhang Q, et al. (2006) STAT3 induces transcription of the DNA methyltransferase 1 gene (DNMT1) in malignant T lymphocytes. Blood 108(3):1058-1064), functions to maintain both hematopoietic and leukemic stem cells. CSCs in glioblastoma and breast cancer require STAT3 activation (see, Marotta L L, et al. (2011) The JAK2/STAT3 signaling pathway is required for growth of CD44(+)CD24(−) stem cell-like breast cancer cells in human tumors. The Journal of Clinical Investigation 121(7):2723-2735; and Sherry M M, et al. (2009) STAT3 is required for proliferation and maintenance of multipotency in glioblastoma stem cells. Stem Cells 27(10):2383-2392) resulting from IL-6 or EGFR (Yang J, et al. (2013) Tumor-associated macrophages regulate murine breast cancer stem cells through a novel paracrine EGFR/Stat3/Sox-2 signaling pathway. Stem Cells 31(2):248-258).

Also, trastuzumab (HER-2-specific monoclonal antibody) resistance in HER2+ breast tumors occurs by IL-6-driven expansion of stem-like cells. In other cases, STAT3 activation in CSCs is due to Runx1-mediated silencing of SOCS family members. STAT3 additionally promotes CSCs via tumor-stromal interactions. Breast cancer cells secrete factors that activate STAT3 in cancer-associated fibroblasts, which respond by producing CCL2 to induce CSC phenotypes in breast cancer cells (see, Tsuyada A, et al. (2012) CCL2 mediates cross-talk between cancer cells and stromal fibroblasts that regulates breast cancer stem cells. Cancer research 72(11):2768-2779).

STAT3 activation is associated with aggressive clinical behavior and poor prognosis. Interestingly, inhibiting STAT3 can prevent tumor growth in mice without affecting growth of cancer cells in vitro (Hedvat M, et al. (2009) The JAK2 inhibitor AZD1480 potently blocks Stat3 signaling and oncogenesis in solid tumors. Cancer cell 16(6):487-497; and Xie T X, et al. (2004) Stat3 activation regulates the expression of matrix metalloproteinase-2 and tumor invasion and metastasis. Oncogene 23(20):3550-3560). The ability to migrate, invade, and eventually metastasize is a malignant hallmark that enables cancer cells to grow and spread in vivo. Thus, STAT3 has been found to intimately regulate these processes, and in particular, many matrix metalloproteinases (MMPs) are under transcriptional control of STAT3. For example, STAT3 regulation of MMP-2 promotes invasion and metastasis in melanoma and ovarian cancer cells (see, Xie T X et al., supra; Xie T X, et al. (2006) Activation of stat3 in human melanoma promotes brain metastasis. Cancer Research 66(6):3188-3196; and Seo J M, et al. (2012) Leukotriene B4 receptor-2 promotes invasiveness and metastasis of ovarian cancer cells through signal transducer and activator of transcription 3 (STAT3)-dependent up-regulation of matrix metalloproteinase 2. The Journal of Biological Chemistry 287(17):13840-13849), while MMP-7 is critical to pancreatic cancer progression (see, Fukuda A, et al. (2011) Stat3 and MMPI contribute to pancreatic ductal adenocarcinoma initiation and progression. Cancer cell 19(4):441-455).

STAT3 and c-Jun cooperatively induce MMP-1 and MMP-10 in bladder cancer cells to increase motility and tumor formation in mice (see, Itoh M, et al. (2006) Requirement of STAT3 activation for maximal collagenase-1 (MMP-1) induction by epidermal growth factor and malignant characteristics in T24 bladder cancer cells. Oncogene 25(8):1195-1204). Moreover, STAT3C transformation of immortalized breast epithelial cells requires MMP-9, whose expression correlates with STAT3 activation in primary breast cancers (Dechow T N, et al. (2004) Requirement of matrix metalloproteinase-9 for the transformation of human mammary epithelial cells by Stat3-C. Proceedings of the National Academy of Sciences of the United States of America 101(29):10602-10607).

Besides MMPs, genes linked to epithelial-mesenchymal transition (EMT) are regulated by STAT3. For instance, STAT3 directly promotes Snail expression while also inducing LIV1, a zinc transporter essential for Snail nuclear localization (see, Yamashita S, et al. (2004) Zinc transporter LIVI controls epithelial-mesenchymal transition in zebrafish gastrula organizer. Nature 429(6989):298-302; and Yadav A, et al. (2011) IL-6 promotes head and neck tumor metastasis by inducing epithelial-mesenchymal transition via the JAKSTAT3-SNAIL signaling pathway. Molecular Cancer Research: MCR 9(12):1658-1667.=).

Twist is another key EMT gene upregulated by STAT3 (see, Cheng G Z, et al. (2008) Twist is transcriptionally induced by activation of STAT3 and mediates STAT3 oncogenic function. The Journal of biological chemistry 283(21):14665-14673; Pakala S B, et al. (2013) MTA1 promotes STAT3 transcription and pulmonary metastasis in breast cancer. Cancer research; and Cho K H, et al. (2013) STAT3 mediates TGF-beta1-induced TWIST1 expression and prostate cancer invasion. Cancer Letters.). STAT3 mediates EGFR-stimulated Twist expression, E-cadherin downregulation and human colorectal cancer epithelial-mesenchymal transition (EMT), and motility, and levels of Twist correlate with EGFR and STAT3 phosphorylation in primary breast tumors (see, Lo H W, et al. (2007) Epidermal growth factor receptor cooperates with signal transducer and activator of transcription 3 to induce epithelial-mesenchymal transition in cancer cells via up-regulation of TWIST gene expression. Cancer Research 67(19):9066-9076).

In colorectal carcinoma, STAT3 may promote EMT by inducing ZEB1, a repressor of E-cadherin. Transformation of immortalized prostate epithelial cells by STAT3C involves upregulation of integrin β6 and its ligands fibronectin and tenascin C, which produce an EMT phenotype. Reciprocally, HER2 interaction with integrin 134 activates STAT3 to cause loss of epithelial adhesion and polarity. STAT3 also modulates the cytoskeleton to promote migration through both transcriptional and non-transcriptional mechanisms. Angiogenesis is another process crucial to tumor growth in vivo but is not readily assayed in vitro. STAT3 induction of MMPs may facilitate angiogenesis (Xiong H, et al. (2012) Roles of STAT3 and ZEB1 proteins in E-cadherin downregulation and human colorectal cancer epithelial-mesenchymal transition. The Journal of Biological Chemistry 287(8):5819-5832), in addition to their role in motility.

The pro-angiogenic factor VEGF (vascular endothelial growth factor) is a STAT3 target gene. In multiple cancer models, STAT3 regulation of VEGF enhances tumor vascularity, growth, and metastasis in vivo; inhibiting STAT3 or VEGF does the opposite. Interestingly, STAT3 activation in endothelial cells is critical to assuming the angiogenic phenotype (Yahata Y, et al. (2003) Nuclear translocation of phosphorylated STAT3 is essential for vascular endothelial growth factor-induced human dermal microvascular endothelial cell migration and tube formation. The Journal of biological chemistry 278(41):40026-40031) and derives from VEGF itself, alongside other factors secreted by both tumor cells and tumor-infiltrating myeloid cells. Thus, STAT3 activation in tumor cells spreads to stromal cells, fostering tumor growth from multiple cellular compartments. STAT3 in both tumor and stroma can also modulate VEGF indirectly by upregulating HIF-la, which stimulates VEGF transcription (Xu Q, et al. (2005) Targeting Stat3 blocks both HIF-1 and VEGF expression induced by multiple oncogenic growth signaling pathways. Oncogene 24(36):5552-5560; and Niu G, et al. (2008) Signal transducer and activator of transcription 3 is required for hypoxia-inducible factor-lalpha RNA expression in both tumor cells and tumor-associated myeloid cells. Molecular Cancer Research: MCR 6(7):1099-1105).

Tumor growth in vivo requires evading immune destruction. Here, too, the actions of STAT3 in multiple cellular compartments are synergistic, functioning to dampen the immune response and promote tumor tolerance. In both cancer cells and cancer-associated fibroblasts, STAT3 curbs the secretion of chemoattractants and pro-inflammatory cytokines such as TNF-α and IFN-β, while inducing the secretion of immunosuppressive IL-6, IL-10, and TGF-β (see, Burdelya L, et al. (2005) Stat3 activity in melanoma cells affects migration of immune effector cells and nitric oxide-mediated antitumor effects. J Immunol 174(7):3925-3931; Groner B, et al. (2008) The function of Stat3 in tumor cells and their microenvironment. Seminars in cell & developmental biology 19(4):341-350; and Bollrath J & Greten F R (2009) IKK/NF-kappaB and STAT3 pathways: central signaling hubs in inflammation-mediated tumour promotion and metastasis. EMBO Reports 10(12):1314-1319). Furthermore, the maturation and function of immunological cells is impaired by STAT3 activation, which can result from STAT3-dependent secretion of paracrine factors by tumor cells.

In some aspects, determining whether the STAT3 pathway is activated and/or determining whether the level of activation of the STAT3 pathway, e.g., in a cell, is increased, decreased, or not increased, or not decreased, relative to a control (e.g., a cell in which it is known that the STAT3 pathway is not activated, and or a control reference value), includes assessing the levels of STAT3-dependent gene expression. Determining STAT3-dependent gene expression includes determining the expression level of one or more STAT3-regulated genes and/or the level of one or more polypeptides encoded by STAT3-regulated gene(s). The list of STAT3-regulated genes is lengthy, and known in the art. Thus, a complete list of STAT3-regulated genes is not disclosed herein. However, non-limiting examples of STAT3-regulated genes include, e.g., myeloid cell leukemia sequence 1 (BCL2-related) (MCL1), jun B proto-oncogene (JUNB), B-cell CLL/lymphoma 6 (BCL6), nuclear factor, interleukin 3 regulated (NFIL3), calpain 2, (m/II) large subunit (CAPN2), early growth response 1 (EGR1), vascular endothelial growth factor A (VEGF), protein tyrosine phosphatase type IVA, member 1 (PTPCAAX1), Kruppel-like factor 4 (gut) (KLF4), exostosin glycosyltransferase 1 (EXT1), Niemann-Pick disease, type C1 (NPC1), p21 protein (Cdc42/Rac)-activated kinase 2 (PAK2), pericentrin (PCNT), fibrinogen-like 2 (FGL2), angiopoietin 1 (ANGPT1), GRB10 interacting GYF protein 1 (GIGYF1)(also known as PERQ1), ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6), Brother of CDO (BOC), cysteine dioxygenase (CDO), BCL2-like 1 (BCL2L1) (BCLX), CYCLIN D1, baculoviral IAP repeat containing 5 (BIRC5) (also known as SURVIVIN), and B-cell CLL/lymphoma 2 (BCL2) (this exemplary group of genes is referred to herein as “STAT3-regulated genes”) (see also, Alvarez J V, et al. (2005) Identification of a genetic signature of activated signal transducer and activator of transcription 3 in human tumors. Cancer research 65(12):5054-5062). Thus, in some embodiments, the level of STAT3 pathway activation correlates with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides including, e.g., MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and BCL2 (this group of genes is referred to herein collectively as “STAT3 upregulated genes”). In some embodiments, the level of STAT3 pathway activation correlates inversely with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides including, e.g., PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and CDO (this group of genes is referred to herein collectively as “STAT3 downregulated genes.

The GenBank® Accession Nos. for the human nucleic acid sequences of these genes, as well as the human amino acid sequences encoded by those genes are set forth in Table 3, below:

TABLE 3 GenBank ® Accession Nos. Nucleic Acid SEQ ID Amino Acid SEQ ID Gene Name GenBank ® No. NO: GenBank ® No. NO.: MCL1 NM_001197320 13 NP_001184249 14 JUNB NM_002229 15 NP_002220 16 BCL6 NM_001130845 17 NP_001124317 18 NFIL3 NM_005384 19 NP_005375 20 CAPN2 NM_001146068 21 NP_001139540 22 EGR1 NM_001964 23 NP_001955 24 VEGF NM_001025366 25 NP_001020537 26 PTPCAAX1 NM_003463 27 NP_003454 28 KLF4 NM_004235 29 NP_004226 30 EXT1 NM_000127 31 NP_000118 32 NPC1 NM_000271 33 NP_000262 34 PAK2 NM_002577 35 NP_002568 36 PCNT NM_006031 37 NP_006022 38 FGL2 NM_006682 39 NP_006673 40 ANGPT1 NM_001146 41 NP_001137 42 PERQ1 NM_022574 43 NP_072096 44 CLN6 NM_017882 45 NP_060352 46 BOC NM_033254 47 NP_150279 48 CDO NM_001801.2 49 NP_001792.2 50 BCLX, NM_138578 51 NP_612815.1 52 CYCLIN D1 NM_053056 53 NP_444284.1 54 SURVIVIN NM_001168 55 NP_001159 56 BCL2 NM_000633 57 NP_000624 58

Furthermore, in other embodiments, the level of activation of the STAT3 pathway is determined by detecting STAT3 phosphorylation, nuclear localization of STAT3, STAT3 DNA binding, and/or cell surface expression of the protein gp130 (CD130).

In some aspects, the STAT3 phosphorylation comprises phosphorylation of tyrosine 705 of human STAT3. Antibodies for detecting phosphorylation of tyrosine 705 of human STAT3 and gp130 are commercially available, e.g., from Cell Signaling Technology and Santa Cruz Biotechnology.

Methods for determining STAT3 phosphorylation are known in the art, e.g., Western blot. Methods for determining cell surface expression of markers such as gp130 are also known in the art (e.g., flow cytometry), and are described in Example 1, below.

STAT3 DNA binding can be determined by, e.g., electrophoretic mobility shift assay (EMSA), as described in Turkson J. et al. Requirement of Ras/Rac1-mediated p38 and c-Jun N-terminal kinase signaling for Stat3 transcriptional activity induced by the Src oncoprotein. Mol. Cel. Biol. 1999; 19:7519-28. STAT3 DNA binding can also be measured by chromatin immunoprecipitation (ChIP) as described, e.g., in Walker S R et al. STAT5 outcompetes STAT3 to regulate the expression of the oncogenic transcriptional modulator BCL6. Molecular and Cellular Biology 2013; 33:2879-90.

Any of the above markers or combinations of two or more thereof can be used to determine whether the STAT3 pathway is active in a test sample (e.g., in a cancer cell and/or subject with cancer).

Atovaquone-Related Compounds

Provided herein are atovaquone-related compounds and methods of their use. Atovaquone-related compounds include atovaquone itself, as well as other compounds that have both STAT3 and mTOR inhibitory activities. Examples of atovaquone-related compounds include substituted hydroxynaphthoquinone compounds. Suitable substituents on substituted hydroxynaphthoquinone compounds include halogen (e.g., F, Cl, Br, or I), C₁-C₁₀ alkyl, C₃-C₂₀ cycloalkyl, or aryl. In some embodiments, substituents such as C₃-C₂₀ cycloalkyl and aryl can be optionally further substituted with halogen or C₁-C₁₀ alkyl.

In some embodiments, a substituted hydroxynaphthoquinone can be a compound of formula (I):

in which each of R₁, R₂, R₃, and R₄, independently is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen (e.g., F, Cl, Br, or I) or C₁-C₁₀ alkyl.

A subset of the compounds of formula (I) are those in which R₅ is cyclohexyl substituted with aryl (e.g., phenyl), in which aryl is substituted with Cl. In such compounds, each of R₁, R₂, R₃, and R₄ can be H. Examples of such compounds include atovaquone and its cis-isomer.

Another subset of the compounds of formula (I) are those in which R₅ is methyl substituted with cyclohexyl, in which cycloalkyl is substituted with t-butyl or R₅ is n-butyl substituted with decahydronaphthyl. In such compounds, each of R₁, R₂, R₃, and R₄ can be H. Examples of such compounds include buparvaquone and TCBHN described below.

In some embodiments, a substituted hydroxynaphthoquinone can be a compound of formula (II):

in which each of R₁, R₂, R₃, and R₄, independently is H or C₁-C₁₀ alkyl; R₅ is C₁-C₁₀ alkyl optionally substituted with C₃-C₂₀ cycloalkyl, or C₃-C₂₀ cycloalkyl optionally substituted with C₁-C₁₀ alkyl or aryl; and each of C₃-C₂₀ cycloalkyl and aryl, independently, is optionally substituted with halogen or C₁-C₁₀ alkyl.

A subset of the compounds of formula (I) are those in which R₅ is cyclohexyl. In such compounds, each of R₁, R₂, R₃, and R₄ can be H. An example of such compounds is parvaquone described below.

Atovaquone is commercially available (trade name: Mepron). It is an antiprotozoal agent with the chemical name trans-2-[4-(4-chlorophenyl)cyclohexyl]-3-hydroxy-1,4-naphthalenedione. Mepron is formulation as a suspension for oral administration. Each teaspoonful (5 mL) contains 750 mg of atovaquone and the inactive ingredients benzyl alcohol, flavor, poloxamer 188, purified water, saccharin sodium, and xanthan gum.

Other atovaquone-related compounds encompassed herein include atovaquone's isomer (cis-2-[4-(4-chlorophenyl)cyclohexyl]-3-hydroxy-1,4-naphthoquinone), buparvaquone (2((4-tert-butylcyclohexyl)methyl)-3-hydroxy-1,4-naphthoquinone) (Hudson, A. T., et al.: Parasitology, 90, 45 (1985), Dhar, S., et al.: Vet. Rec., 119, 635 (1986)), parvaquone (3-cyclohexyl-4-hydroxy-naphthalene-1,2-dione), and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone (TDBHN).

Also encompassed herein are analogs of the above-disclosed atovaquone-related compounds. Analogs encompassed herein have both STAT3 and mTOR inhibitory activities and, typically, although not necessarily, are structurally related to atovaquone. Methods for designing analogs are also known in the art. The desired activities of the analogs (i.e., both STAT3 and mTOR inhibitory activities and/or ability to induce activation of the eIF2α/ATF4 pathway) can be determined using, e.g., in vitro cell-based or in vivo assays described in detail above (e.g., Q-PCR, immunoprecipitation, Western blot, ELISA, etc.).

The atovaquone-related compounds described herein include the compounds themselves, as well as their pharmaceutically acceptable derivatives, such as salts, prodrugs, and solvates of the atovaquone-related compounds.

A salt of an atovaquone-related compound, for example, can be formed between an anion and a positively charged group (e.g., amino) on the compound. Suitable anions include chloride, bromide, iodide, sulfate, nitrate, phosphate, citrate, methanesulfonate, trifluoroacetate, acetate, malate, tosylate, tartrate, fumurate, glutamate, glucuronate, lactate, glutarate, and maleate. Likewise, a salt can also be formed between a cation and a negatively charged group (e.g., carboxylate) on the compound. Suitable cations include sodium ion, potassium ion, magnesium ion, calcium ion, and an ammonium cation such as tetramethylammonium ion. The salts of the atovaquone-related compounds described herein also include those containing quaternary nitrogen atoms.

Examples of prodrugs of the atovaquone-related compounds described herein include esters and other derivatives, which, upon administration to a subject, are capable of providing active atovaquone-related compounds. A solvate refers to a complex formed between an active atovaquone-related compound and a pharmaceutically acceptable solvent. Examples of pharmaceutically acceptable solvents include water, ethanol, isopropanol, ethyl acetate, acetic acid, and ethanolamine.

Also within the scope of this disclosure is a pharmaceutical composition containing one or more of the atovaquone-related compounds described herein for use in treating cancer, and the use of such a composition for the manufacture of a medicament for the just-mentioned treatment.

Uses of Atovaquone-Related Compounds

It is presently discovered that atovaquone-related compounds inhibit STAT3 and mTOR pathways, as well as induce activation of the eIF2α/ATF4 pathway, and can be used for the treatment of cancer, as well as related benefits (e.g., determining whether a cancer is susceptible to treatment with an atovaquone-related compound, methods of monitoring efficacy of treatment with an atovaquone-related compound, etc.)

Cancers that can be treated according to the methods disclosed herein include, but are not limited to cancers with increased levels of activation of the STAT3 and/or mTOR pathways. Non-limiting examples included, e.g., solid such as breast cancer, melanoma, lung cancer, ovarian cancer, pancreatic cancer, colorectal cancer, prostate cancer, brain cancer, gastroesophageal cancer, kidney cancer; endometrial cancer, non-small cell lung cancer, neuroendocrine cancers, as well as glioblastoma multiforme, or a hematological cancer such as acute myeloid leukemia, chronic myeloid leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma, acute lymphoblastic leukemia, and chronic lymphocytic leukemia.

Provided herein are methods of decreasing the growth of a cancer cell, the method comprising delivering to a target cancer cell a growth-inhibitory amount of an atovaquone-related compound (e.g., atovaquone, TDBHN, parvaquone, buparvaquone, etc.) (e.g., administering the compound to a cancer cell (e.g., a mammalian, e.g., human, cancer cell) or to a subject (e.g., mammal, e.g., human, subject) with cancer), wherein, prior to the delivery, an increased level of activation of the mTOR pathway in the cancer (e.g., in a test cell of or from the cancer) compared to a control level of activation of the mTOR pathway (e.g., in a control sample of or from a control cell) has been found. Further, in some aspects, prior to the delivery, an increased level of activation of the STAT3 pathway in the cancer compared to a control level of activation of the STAT3 pathway has also been found. An increased level of activation of the mTOR and/or STAT3 pathways means that level of expression of the one or more of the markers used to determine that the pathway is activated (described above) is upregulated by at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 75, or 100-fold or more relative to a control level.

In some aspects, suitable control levels include, e.g., a predetermined value based on the expression level of the relevant marker(s) in one or more cancer-free individuals. Alternatively, or, in addition, the control level can be simultaneously or sequentially (either before or after) determined when the level in cancer is determined, e.g. in the same assay in which the cancer is tested, wherein the results are directly compared. A control level can also be the level in a sample (e.g., exosomes and/or microvesicles from a body fluid or a sample of or from one or more cancer cells) obtained from a subject prior to treatment with an atovaquone-related compound. Moreover, a control level can be the level in a sample of the tissue from the subject in which the cancer is located but in which no cancer cells are detectable, in a sample of the same tissue but in a different organ of the subject, or in a sample from the subject of a different tissue.

Also provided herein are methods of determining the susceptibility of a cancer (e.g., the cancers described above) in a subject to the growth-inhibitory effect of an atovaquone-related compound (e.g., atovaquone), the method comprising, assessing the level of activation of the mTOR pathway in a test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of atovaquone if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of atovaquone if an increased level activation of the mTOR pathway is not detected in the test sample compared to a control level of activation of the mTOR pathway than if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway. In some aspects, the method further comprises assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of atovaquone if an increased level of activation of the STAT3 is detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of atovaquone if an increased level of activation of the STAT3 pathway is not detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway than if an increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample compared to a control level of activation of the mTOR pathway. In further aspects, the methods can further comprise administering an atovaquone-related compound to the subject if the increased level activation of the mTOR pathway is detected in the test sample. In some aspects, the method comprises administering an atovaquone-related compound to the subject if the increased level of activation of the mTOR pathway is detected in the test sample, if the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample, or if the increased level activation of the mTOR pathway is detected in the test sample and the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample.

In some aspects, the test sample is a sample of or from one or more cancer cells from the subject. In some aspects, the second test sample is a sample of or from one or more cancer cells from the subject.

In some aspects, the level of activation of the mTOR pathway is determined to be increased in the test sample relative to a control sample if the difference is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold. By way of non-limiting example, in one embodiment, if the expression level of REDD1, CHOP, ATF3, CHAC1, and/or ATF4 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in the test sample relative to the control, then it is determined that the mTOR pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound. As another non-limiting example, if the level of phosphorylation of one or more of the following polypeptides: mTOR, ribosomal protein S6, S6 kinase, 4E-BP1, eIF2α, is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in a test sample, relative to a control sample then it is determined that the mTOR pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound. Methods for determining the level of activation of the mTOR pathway (e.g., by determining the expression levels of one or more of the markers described above), are described above.

In some aspects, the level of activation of the STAT3 pathway is determined to be increased in the test sample relative to a control sample if the difference is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold. By way of non-limiting example, in one embodiment, if the expression level of MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and/or BCL2 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in the test sample relative to the control, then it is determined that the STAT3 pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound. By way of non-limiting example, in one embodiment, if the expression level of PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and/or CDO is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold decreased in the test sample relative to the control, then it is determined that the STAT3 pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound. As another non-limiting example, if the level of phosphorylation of STAT3 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in a test sample, relative to a control sample then it is determined that the STAT3 pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound. Moreover, if nuclear localization of STAT-3, STAT-3 DNA binding, and/or STAT3-dependent gene expression is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased, then it is determined that the STAT3 pathway is increased, and the cancer cell is susceptible to treatment with an atovaquone-related compound.

Methods for determining the level of activation of the mTOR pathway and/or STAT3 pathway (e.g., by determining the expression levels of one or more of the markers described above), are described above.

In other aspects, provided herein are methods of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound (e.g., atovaquone) in a subject, the method comprising, assessing the level of activation of the mTOR pathway in a test sample from a subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is lower than the level of activation of the mTOR pathway in a control sample, and not identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is not lower than the level of activation of the mTOR pathway in a control sample. In some aspects, the method further comprises assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is lower than the level of activation of the STAT3 pathway in a control sample or a second control sample, and not identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is not lower than the level of activation of the STAT3 pathway in the control sample or the second control sample.

In some aspects, the test sample is a sample of or from one or more cancer cells from the subject. In some aspects, the control sample or the second control sample was obtained from the subject prior to the treatment with the atovaquone-related compound.

Also provided herein are methods of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound in a subject are provided, wherein the method comprises: (a) assessing the level of activation of the eIF2α/ATF4 pathway in a test sample from a subject that has been treated with the compound, (b) identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is increased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample, and (c) not identifying the treatment as having been successful if the level of activation of the eIF2α/ATF4 pathway in the test sample is not increased relative to the level of activation of the eIF2α/ATF4 pathway in a control sample. In some embodiments, the method further comprises determining the level of expression of CHOP and/or CHAC1 and/or REDD1, wherein increased expression of one or both of the genes or the polypeptides encoded by these genes correlates with activation of the eIF2α/ATF4 pathway. In some aspects, the level of activation of the eIF2α/ATF4 pathway is determined to be increased in the test sample relative to a control sample if the difference is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold. In some aspects, the method comprises determining the level of phosphorylation of eIF2α, wherein its increased phosphorylation correlates with activation of the eIF2α/ATF4 pathway. In some aspects, the level of phosphorylation is determined to be increased relative to the control (e.g., a sample obtained prior to treatment with an atovaquone-related compound), if the level of phosphorylated protein is increased by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold. In other aspects, the method comprises determining the expression level of ATF4, wherein increased expression of ATF4 or the polypeptide encoded by ATF4 correlates with activation of the eIF2α/ATF4 pathway. In some aspects, the level of expression of ATF4 is determined to be increased relative to the control (e.g., a sample obtained prior to treatment with an atovaquone-related compound), if the level of expression of ATF4 is increased by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold.

In some aspects, the level of expression of CHOP is determined to be increased relative to the control (e.g., a sample obtained prior to treatment with an atovaquone-related compound), if the level of expression of CHOP is increased by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold.

In some aspects, the level of expression of CHAC1 is determined to be increased relative to the control (e.g., a sample obtained prior to treatment with an atovaquone-related compound), if the level of expression of CHAC1 is increased by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold.

In some aspects, the level of expression of REDD1 is determined to be increased relative to the control (e.g., a sample obtained prior to treatment with an atovaquone-related compound), if the level of expression of REDD1 is increased by at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold.

Also provided herein are methods of treating cancer in a patient, the method comprising: administering a therapeutically effective amount of an atovaquone-related compound to a patient in need thereof; and, after the administration, monitoring the level of activation of the mTOR pathway in a test sample or two more serial test samples from the patient. In some aspects, the method further comprises, after the administration, monitoring the level of activation of the STAT3 pathway in the test sample, the two or more (e.g., three, four, five, six, seven, eight, nine, ten, or more) serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects, the method further comprises continuing the treatment if the level of activation of the mTOR pathway in the test sample or the two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects, the method further comprises continuing the treatment if the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some embodiments, these treatment methods can follow or be followed by steps including, e.g., diagnosing the patient (e.g., with cancer) and/or making a prognosis and/or determining whether the treatment method (e.g., treatment with an atovaquone-related compound) is likely to be successful for treating the cancer (e.g., if the cancer is likely susceptible to treatment with the atovaquone-related compound), as described herein.

In other aspects, also provided herein are methods of treating cancer in a patient, the method comprising: administering a therapeutically effective amount of an atovaquone-related compound to a patient in need thereof; and, after the administration, monitoring the level of activation of the eIF2α/ATF4 pathway in a test sample or two or more serial test samples from the patient. In some aspects, the method further comprises determining the level of expression of CHOP and/or CHAC1 and/or REDD1. In some aspects, the method further comprises, after the administration, monitoring the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects, the method further comprises, after the administration, monitoring the level of activation of the mTOR pathway in the test sample, the two or more serial test samples, a second test sample or a second set of two or more serial test samples from the patient. In some aspects, the method further comprises continuing the treatment if the level of activation of the eIF2α/ATF4 pathway and/or the expression level of CHOP and/or CHAC1 and/or REDD1 in the test sample or the two or more serial test samples is increased (e.g., by at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 75, or 100-fold or more) relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects, the method further comprises continuing the treatment if the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. In some aspects, the method further comprises continuing the treatment if the level of activation of the mTOR pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment. Serial sets of test samples as disclosed herein can be taken at any frequency (e.g., every hour, every 12 hours, once a day, every other day, once a week, once a month, once every two, three, four, five, six, or nine months, or once a year) for as long as considered necessary (e.g., a day, several days, a week, a month, 6 months, a year, or longer). Moreover, times between taking of the samples can the same or different.

In some aspects, the test sample or each of the two or more serial test samples is a sample of or from one or more cancer cells from the subject. In some aspects, the second set of two or more serial test samples comprises a sample of or from one or more cancer cells from the subject. In other aspects, the control sample is obtained from non-autologous mammalian cancer cells (preferably of the same species as the test sample) known to have activated mTOR and/or STAT3 pathway(s) and/or known to not have activated eIF2α/ATF4 pathway.

In some aspects, the cancer cell growth inhibitory therapy or cancer treatment (i.e., “the treatment”) is identified as having been successful if the level of activation of the mTOR pathway in the test sample is decreased, relative to the control sample, by at least 2-fold, at least 3-fold, at least 5-fold, at least 10-fold, or more. By way of non-limiting example, in one embodiment, if the expression level of REDD1, CHOP, ATF3, CHAC1, and/or ATF4 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in the test sample relative to the control, then it is determined that the treatment has been successful. As another non-limiting example, if the level of phosphorylation of one or more of the following polypeptides: mTOR, ribosomal protein S6, S6 kinase, 4E-BP1, eIF2α, at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold decreased in the test sample, relative to the control sample then it is determined that the has been successful. Methods for determining the level of activation of the mTOR pathway (e.g., by determining the expression levels of one or more of the markers described above), are described above.

In some aspects, the treatment is identified as having been successful if the level of activation of the STAT3 pathway in the test sample is decreased, relative to the control sample, by at least 2-fold, at least 3-fold, at least 5-fold, at least 10-fold, or more. In some aspects, the level of activation of the STAT3 pathway is determined to be increased in the test sample relative to a control sample if the difference is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold. If the level of the STAT3 pathway is not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful). By way of non-limiting example, in one embodiment, if the expression level of MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and/or BCL2 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold decreased in the test sample relative to the control sample, then it is determined that the treatment has been successful. If the levels of MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and/or BCL2 are not decreased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful). By way of non-limiting example, in one embodiment, if the expression level of PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and/or CDO is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold increased in the test sample relative to the control sample, then it is determined that the treatment has been successful. If the levels of the PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and/or CDO is not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful). As another non-limiting example, if the level of phosphorylation of STAT3 is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold decreased in the test sample, relative to the control sample, then it is determined that treatment has been successful. If the level of STAT3 phosphorylation is not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful). Moreover, if nuclear localization of STAT-3, STAT-3 DNA binding, STAT3-dependent gene expression, and/or cell surface expression of the protein gp130 (CD130) is at least 2, 3, 4, 5, 6, 7, 8, 9, or 10-fold decreased, then it is determined that the treatment has been successful. If the level of the nuclear localization of STAT-3, STAT-3 DNA binding, STAT3-dependent gene expression, and/or cell surface expression of the protein gp130 (CD130) is not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful).

In another aspect, the effect of an atovaquone-related compound in a subject is determined by determining whether the levels of eIF2α phosphorylation and ATF4 are increased relative to a control sample. If the levels of phospho-eIF2α and/or ATF4 are increased (e.g., at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, or more) in a test sample relative to a control sample then the treatment with an atovaquone-related compound is expected to have the desired therapeutic effect (e.g., inhibition of the mTOR pathway, e.g. treatment of cancer). If the levels of phospho-eIF2α and/or ATF4 are not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has had the desired therapeutic effect (inhibition of the mTOR pathway, e.g. treatment of cancer), or it is determined that it has not had the desired therapeutic effect). In some embodiments, if the levels of CHOP and/or CHAC1 and/or REDD1 are increased (e.g., at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 10-fold, or more) in a test sample relative to a control sample, then it is determined that the treatment with an atovaquone-related compound has been successful. If the level of CHOP and/or CHAC1 and/or REDD1 is not increased in a test sample relative to a control sample, then it is not determined that the treatment with an atovaquone-related compound has been successful (or it is determined that it has not been successful).

In any of the above methods, the test sample(s) can be obtained from microvesicles or exosomes obtained from a body fluid of a subject with the cancer and the control sample(s) can be obtained from microvesicles or exosomes obtained from a control sample of the body fluid. In some aspects, the body can be blood, lymph, or urine, or other appropriate body fluid, e.g., cerebrospinal fluid (CSF), ascites, and pleural fluid. In other aspects, the test sample can be obtained from a tumor biopsy.

Any of the above described methods of treatment can further comprise administering to the subject (e.g., a subject in which the efficacy of the treatment with an atovaquone-related compound was determined to be poor or not optimal, or a subject in which initial treatment with an atovaquone-related compound produced tumor-inhibitory effects but the subject subsequently developed resistance to the treatment) an additional therapy for the treatment of cancer. Further, any of the treatment methods described herein can follow or be followed by steps including, e.g., diagnosing the patient (e.g., with cancer) and/or making a prognosis and/or determining whether the treatment method (e.g., treatment with an atovaquone-related compound) is likely to be successful for treating the cancer (e.g., if the cancer is likely susceptible to treatment with the atovaquone-related compound), as described herein.

In other embodiments, the methods can comprise recording the results in a database or medical history (e.g., medical records) of the subject, selecting the subject for increased monitoring or periodically monitoring the health of the subject (e.g., for development or changes in the signs or symptoms of the breast cancer, e.g., tumor development and/or changes in tumor size (e.g., increased or decreased size), such as e.g., clinical exam, mammography, MRI, or other suitable imaging or other diagnostic method(s) known in the art. In other embodiments, the methods can comprise using a PCR machine to determine the level of expression of one or more markers of activation of the mTOR and/or STAT3 and/or eIF2α/ATF4 pathways.

In the above-described methods for cancer cell growth inhibitory therapy and treatment of cancer, the method can further comprise administering an additional therapy to the patient. Additional therapies can include an additional treatment for cancer (e.g., chemotherapy (e.g., administering a chemotherapeutic agent), administering a biologic agent, e.g., antigen, vaccine, antibody etc., administering a cytokine, radiation therapy, immunotherapy, and/or surgery, etc.). Such combination therapy can be sequential therapy wherein the patient is treated first with one therapy and then the other, and so on, or all therapies can be administered simultaneously. In either case, these therapies are said to be coadministered. It is to be understood that “coadministered” does not necessarily mean that the drugs and/or therapies are administered in a combined form (i.e., they may be administered separately or together to the same or different sites at the same or different times).

In some embodiments, an atovaquone-related compound can be used for the treatment of cancer, either as initial therapy or as a second-line option if resistance to another therapy (e.g., JAK resistance mutations emerge following JAK inhibitor therapy) develops.

Chemotherapeutic agents, which can be administered in a combination therapy with an atovaquone-related compound, include for example: taxanes such as taxol, taxotere or their analogues; alkylating agents such as cyclophosphamide, isosfamide, melphalan, hexamethylmelamine, thiotepa or dacarbazine; antimetabolites such as pyrimidine analogues, for instance 5-fluorouracil, cytarabine, capecitabine, and gemcitabine or its analogues such as 2-fluorodeoxycytidine; folic acid analogues such as methotrexate, idatrexate or trimetrexate; spindle poisons including vinca alkaloids such as vinblastine, vincristine, vinorelbine and vindesine, or their synthetic analogues such as navelbine, or estramustine and a taxoid; platinum compounds such as cisplatin; epipodophyllotoxins such as etoposide or teniposide; antibiotics such as daunorubicin, doxorubicin, bleomycin or mitomycin, enzymes such as L-asparaginase, topoisomerase inhibitors such as topotecan or pyridobenzoindole derivatives; and various agents such as procarbazine, mitoxantrone, and biological response modifiers or growth factor inhibitors such as interferons or interleukins. Other chemotherapeutic agents include, though are not limited to, a p38/JAK kinase inhibitor, e.g., SB203580; a phospatidyl inositol-3 kinase (PI3K) inhibitor, e.g., LY294002; a MAPK inhibitor, e.g. PD98059; a JAK inhibitor, e.g., AG490; preferred chemotherapeutics such as UCN-01, NCS, mitomycin C (MMC), NCS, and anisomycin; taxoids in addition to those describe above (e.g., as disclosed in U.S. Pat. Nos. 4,857,653; 4,814,470; 4,924,011, 5,290,957; 5,292,921; 5,438,072; 5,587,493; European Patent No. 0 253 738; and PCT Publication Nos. WO 91/17976, WO 93/00928, WO 93/00929, and WO 96/01815. In other embodiments, a cancer therapy can include but is not limited to immunotherapy such as the administration of cytokines and growth factors such as interferon (IFN)-gamma, tumor necrosis factor (TNF)-alpha, TNF-beta, and/or similar cytokines, or an antagonist of a tumor growth factor (e.g., TGF-β and IL-10). Antiangiogenic agents that can be used in the therapy of cancer, include, e.g., endostatin, angiostatin, TNP-470, Caplostatin (Stachi-Fainaro et al., Cancer Cell 7(3), 251 (2005)). Drugs that interfere with intracellular protein synthesis can also be used in the methods of the present disclosure; such drugs are known to those skilled in the art and include puromycin, cycloheximide, and ribonuclease.

For radiation therapy, common sources of radiation used for cancer treatment include, but are not limited to, high-energy photons that come from radioactive sources such as cobalt, cesium, iodine, palladium, or a linear accelerator, proton beams; neutron beams (often used for cancers of the head, neck, and prostate and for inoperable tumors), x or gamma radiation, electron beams, etc.

It is well known that radioisotopes, drugs, and toxins can be conjugated to antibodies or antigen-binding antibody fragments which specifically bind to markers which are produced by or associated with cancer cells, and that such antibody conjugates can be used to target the radioisotopes, drugs or toxins to tumor sites to enhance their therapeutic efficacy and minimize side effects. Examples of these agents and methods are reviewed in Wawrzynczak and Thorpe (in Introduction to the Cellular and Molecular Biology of Cancer, L. M. Franks and N. M. Teich, eds, Chapter 18, pp. 378-410, Oxford University Press. Oxford, 1986), in Immunoconjugates: Antibody Conjugates in Radioimaging and Therapy of Cancer (C. W. Vogel, ed., 3-300, Oxford University Press, N.Y., 1987), in Dillman, R. O. (CRC Critical Reviews in Oncology/Hematology 1:357, CRC Press, Inc., 1984), in Pastan et al. (Cell 47:641, 1986) in Vitetta et al. (Science 238:1098-1104, 1987) and in Brady et al. (Int. J. Rad. Oncol. Biol. Phys. 13:1535-1544, 1987). Other examples of the use of immunoconjugates for cancer and other forms of therapy have been disclosed, inter alia, in U.S. Pat. Nos. 4,331,647, 4,348,376, 4,361,544, 4,468,457, 4,444,744, 4,460,459, 4,460,561 4,624,846, 4,818,709, 4,046,722, 4,671,958, 4,046,784, 5,332,567, 5,443,953, 5,541,297, 5,601,825, 5,637,288, 5,677,427, 5,686,578, 5,698,178, 5,789,554, 5,922,302, 6,187,287, and 6,319,500. In addition, unconjugated antibodies (e.g., antibodies to epidermal growth factor receptors such a HER2/neu) can be used for the treatment of cancer. Exemplary cancer-cell specific antibodies that can be used in the combination therapies disclosed herein are described, for example, in the review by Scott et al. (Nature Reviews Cancer 12, 278-287 (April 2012)). See also, Weiner, L. M., et al. Monoclonal antibodies: versatile platforms for cancer immunotherapy. Nature Rev. Immunol. 10, 317-327 (2010); Beatty, G. L. et al. CD40 agonists alter tumor stroma and show efficacy against pancreatic carcinoma in mice and humans. Science 331, 1612-1616 (2011); Musolino, A. et al Immunoglobulin G fragment C receptor polymorphisms and clinical efficacy of trastuzumab-based therapy in patients with HER-2/neu-positive metastatic breast cancer. J. Clin. Oncol. 26, 1789-1796 (2008); Ferris, R. L., et al. Tumor antigen-targeted, monoclonal antibody-based immunotherapy: clinical response, cellular immunity, and immunoescape. J. Clin. Oncol. 28, 4390-4399 (2010); and Scott, A. M. et al. A Phase I clinical trial with monoclonal antibody ch806 targeting transitional state and mutant epidermal growth factor receptor. Proc. Natl Acad. Sci. USA 104, 4071-4076 (2007).

Other therapies include, e.g., hematopoietic stem cell transplant (HSCT), e.g., for treatment of acute myeloid leukemia (AML) patients and many other cancers.

Formulations, Administration and Dosage

While it is possible to use an inhibitor or agonist disclosed herein for therapy as is, it may be preferable to administer an inhibitor or agonist as a pharmaceutical formulation, e.g., in admixture with a suitable pharmaceutical excipient, diluent, or carrier selected with regard to the intended route of administration and standard pharmaceutical practice. Pharmaceutical formulations comprise at least one active compound, or a pharmaceutically acceptable derivative thereof, in association with a pharmaceutically acceptable excipient, diluent, and/or carrier. The excipient, diluent and/or carrier must be “acceptable,” as defined above. The compositions disclosed herein can be formulated for administration in any convenient way for use in human or veterinary medicine.

Compositions and formulations comprising an atovaquone-related compound disclosed herein, can be administered topically, parenterally, orally, by inhalation, as a suppository, or by other methods known in the art. The term “parenteral” includes injection (for example, intravenous, intraperitoneal, epidural, intrathecal, intramuscular, intraluminal, intratracheal or subcutaneous). Exemplary routes of administration include, e.g., intravenous, intraductal, and intratumoral.

Administration of a composition or formulation disclosed herein can be once a day, twice a day, or more often. Frequency may be decreased during a treatment maintenance phase of the disease or disorder, e.g., once every second or third day instead of every day or twice a day. The dose and the administration frequency will depend on the clinical signs, which confirm maintenance of the remission phase, with the reduction or absence of at least one or more preferably more than one clinical signs of the acute phase known to the person skilled in the art. More generally, dose and frequency will depend in part on recession of pathological signs and clinical and subclinical symptoms of a disease condition or disorder contemplated for treatment with the present compounds.

It will be appreciated that the amount of an atovaquone-related compound for use in treatment will vary with the route of administration, the nature of the condition for which treatment is required, and the age, body weight and condition of the patient, and will be ultimately at the discretion of the attendant physician or veterinarian. Compositions will typically contain an effective amount of the active agent(s), alone or in combination. Preliminary doses can be determined according to animal tests, and the scaling of dosages for human administration can be performed according to art-accepted practices.

Length of treatment, i.e., number of days, will be readily determined by a physician treating the subject; however the number of days of treatment may range from 1 day to about 20 days. In some embodiments, an atovaquone-related compound can be administered in multiple “cycles” with rest periods of 7 days between cycles of administration, or, given the minimal toxicity, continuous indefinite treatment with an atovaquone-related compound is also possible. As provided by the present methods, and discussed below, the efficacy of treatment can be monitored during the course of treatment to determine whether the treatment has been successful, or whether additional (or modified) treatment is necessary.

In some embodiments, an atovaquone-related compound, as described herein, can be formulated with at least one additional therapy (e.g., drug therapy, e.g., chemotherapy, immunotherapy, or other cancer therapy involving administration of a drug) described herein. Thus, formulations can comprise combinations of 2 or more, 3 or more, 4 or more, or 5 or more additional therapies. In certain embodiments, the atovaquone-related compound and the additional therapy (drug) are formulated in separate compositions.

In some aspects, a cancer cell growth-inhibitory amount and/or a therapeutically effective amount of atovaquone is in a range of about 0.5 to about 500 mg/kg/day, about 1 to about 250 mg/kg/day, about 5 to about 125 mg/kg/day, about 5 to about 100 mg/kg/day, or about 10 to about 75 mg/kg/day, about 10 to about 50 mg/kg/day, or about 10 to about 40 mg/kg per day.

In one embodiment, the dose of atovaquone is 1500 mg per day.

Kits

In certain embodiments, kits are provided for treating breast cancer. In still other embodiments, kits are provided for determining the efficacy of a cancer therapy.

In some embodiments, the kits comprise an atovaquone-related compound (e.g., atovaquone, buparvaquone, parvaquone, TDBHN, etc.) for use in the treatment of cancer. In other embodiments, the kits comprise reagents for the detection of the expression level of STAT3 and/or mTOR and/or eIF2α/ATF4 pathways and, optionally, an atovaquone-related compound. Such kits can further comprise instructions to administer the atovaquone-related compound to a subject with cancer if the subject has elevated expression levels of the mTOR and/or prior to treatment. The instructions can further comprise directions to serially test (i.e. test at least once more, at least twice more, at least three time more, etc.) samples obtained from the subject following initiation of treatment with the atovaquone related compound to monitor efficacy of the treatment, wherein the instructions instruct the user (e.g., physician) that treatment is effective if the level of activation of the mTOR pathway is decreased relative to its level of activation prior to treatment and/or if the level of activation of the STAT3 pathway is decreased relative to its level of activation prior to treatment and/or if the level of activation of the eIF2α/ATF4 is increased relative to its level of activation prior to treatment. Method for determining changes in the level of activation of these pathways are described in detail above.

The kits, regardless of type, will generally comprise one or more containers into which the biological agents (e.g. inhibitors) are placed and, preferably, suitably aliquotted. The components of the kits may be packaged either in aqueous media or in lyophilized form.

In accordance with the present invention, there may be employed conventional molecular biology, microbiology, recombinant DNA, immunology, cell biology and other related techniques within the skill of the art. See, e.g., Sambrook et al., (2001) Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y.; Sambrook et al., (1989) Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, N.Y.; Ausubel et al., eds. (2005) Current Protocols in Molecular Biology. John Wiley and Sons, Inc.: Hoboken, N.J.; Bonifacino et al., eds. (2005) Current Protocols in Cell Biology. John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al., eds. (2005) Current Protocols in Immunology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coico et al., eds. (2005) Current Protocols in Microbiology, John Wiley and Sons, Inc.: Hoboken, N.J.; Coligan et al., eds. (2005) Current Protocols in Protein Science, John Wiley and Sons, Inc.: Hoboken, N.J.; Enna et al., eds. (2005) Current Protocols in Pharmacology John Wiley and Sons, Inc.: Hoboken, N.J.; Hames et al., eds. (1999) Protein Expression: A Practical Approach. Oxford University Press: Oxford; Freshney (2000) Culture of Animal Cells: A Manual of Basic Technique. 4th ed. Wiley-Liss; among others. The Current Protocols listed above are updated several times every year.

The following examples are meant to illustrate, not limit, the invention.

EXAMPLES Example 1 Materials and Methods

The following are the materials and methods used in the Examples set forth below.

Connectivity Map Analysis The 12-gene STAT3 signature described in Alvarez J V, et al. ((2005)

Identification of a genetic signature of activated signal transducer and activator of transcription 3 in human tumors. Cancer research 65(12):5054-5062) was mapped from murine U74Av2 probes to all corresponding human U133A probes using a file downloaded from dChip (http://www.hsph.harvard.edu/cli/complab/dchip/common%20HG-U133A_MG-U74Av2.xls). Two genes downregulated by STAT3 activation were similarly mapped. The resulting probe lists shown in Table 4, below, were used to query the Connectivity Map. Detailed results were downloaded, and the “up” score was averaged across all instances for each compound; compounds with fewer than 3 instances were excluded.

TABLE 4 Probe List Up tags Down tags 200730_s_at 202951_at 200731_s_at 216727_at 200732_s_at 212811_x_at 200733_s_at 209610_s_at 200796_s_at 209611_s_at 200797_s_at 212810_s_at 200798_x_at 201473_at 201693_s_at 201694_s_at 201995_at 202679_at 203140_at 203574_at 205962_at 208683_at 208743_s_at 208875_s_at 208876_s_at 208877_at 208878_s_at 210512_s_at 210513_s_at 211527_x_at 212171_x_at 214056_at 214057_at 214888_at 215990_s_at 220266_s_at 221841_s_at

Cell Lines and Tissue Culture

Mouse embryonic fibroblasts (MEFs) were cultured in DMEM+10% FBS. TSC2-null (see, Zhang et al. J Clin Invest. 2003; 112(8):1223-1233) and REDD1-null (see, Sofer et al. Mol. Cell. Biol. July 2005 vol. 25 no. 14 5834-5845) MEFs, along with MEFs from the littermate controls, were kind gifts from Dr. John Blenis and Dr. Leif Ellisen, respectively. HEL (see, Iwama et al. Mol. Cell. Biol. June 1999 vol. 19 no. 6 3940-3950) was a kind gift of Dr. Daniel G. Tenen and grown in RPMI-1640+10% FBS. OCI-AML2 and OCI-AML3 (see, Grunberger et al. Blood Dec. 1, 2003 vol. 102 no. 12 4153-4158), and MOLM-13 (German Collection of Microorganisms and Cell Cultures (DSMZ, Braunschweig, Germany)) were kind gifts of Dr. James D. Griffin and grown in RPMI-1640+10% FBS. MM.1S (ATCC) was a kind gift of Dr. Kenneth C. Anderson and grown in RPMI-1640+10% FBS. SET2 (see, Koppikar et al. Nature 489, 155-159 (6 Sep. 2012)) was a kind gift of Dr. Ross L. Levine and grown in RPMI-1640+10% FBS. HL60 (ATCC) was a kind gift of Dr. James D. Griffin and grown in RPMI-1640+10% FBS. SKBR3, MDA-MB-468, U266, INA-6, RPMI-8226, K562, and MV-4-11 cells were obtained and cultured as previously reported (see, Nelson E A, et al. (2011) The STAT5 inhibitor pimozide decreases survival of chronic myelogenous leukemia cells resistant to kinase inhibitors. Blood 117(12):3421-3429; Nelson E A, et al. (2008) Nifuroxazide inhibits survival of multiple myeloma cells by directly inhibiting STAT3. Blood 112(13):5095-5102; Nelson E A, et al. (2012) The STAT5 Inhibitor Pimozide Displays Efficacy in Models of Acute Myelogenous Leukemia Driven by FLT3 Mutations. Genes & Cancer 3(7-8):503-511; Walker S R, Chaudhury M, Nelson E A, & Frank D A (2010) Microtubule-targeted chemotherapeutic agents inhibit signal transducer and activator of transcription 3 (STAT3) signaling. Molecular Pharmacology 78(5):903-908; and Walker S R, et al. (2009) Reciprocal effects of STAT5 and STAT3 in breast cancer. Molecular Cancer Research: MCR 7(6):966-976). Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donors by Ficoll density gradient centrifugation and maintained in RPMI-1640+10% FBS. All cells were maintained in a humidified incubator at 37° C. with 5% CO₂.

Total RNA Isolation

Cell pellets were lysed in 270 μl RLT Plus buffer (Qiagen, Valencia, Calif.)+1% β-mercaptoethanol and processed by QIAshredder and genomic DNA eliminator spin columns. The flow-through solution was mixed with 460 μl 95% ethanol by pipetting up and down, and then run through an RNeasy spin column (Qiagen). The spin column was washed twice with 500 μl RPE buffer (after ethanol addition), spun once again to remove residual ethanol, and then eluted with 50 μl RNase-free water. All spin steps were performed on a benchtop microcentrifuge at room temperature and 14,000 RPM for 1 minute.

Gene Expression Analysis

Total RNA was reverse transcribed using random hexamers and assayed by qRT-PCR as previously described (see, Grivennikov S I, Greten F R, & Karin M (2010) Immunity, inflammation, and cancer. Cell 140(6):883-899). Primer sequences used are shown in Table 5, below.

TABLE 5 Primer Sequences SEQ SEQ Forward ID Reverse ID Gene (5′→3′) NO (5′→3′) NO 18S GTAACCCGTT 59 CCATCCAATC 60 rRNA GAACCCCATT GGTAGTAGCG Beta TCCCTGGAGA 61 AGCACTGTGT 62 actin AGAGCTACGA TGGCGTACAG Pri-miR- ATTCAGGGTT 63 GGGGCTTTCT 64 146b TTGGGGAGAT GAGCTAAAGG STAT3 ACCGGCGTCCA 65 CCGGGATCCTC 66 GTTCACTACT TGAGAGCTGC SOCS3 TCAAGACCTT 67 TGACGCTGAG 68 CAGCTCCAAG CGTGAAGAAG BIRC3 GGGAAGAGGAG 69 TCCAGGATTGG 70 AGAGAAAGAGC AATTACACAAG NFKB2 AGAGGGAGGA 71 CAGGTTCTGC 72 GGGCCTTTAG TTCCCAGAAT RELB AGCATCCTT 73 AGGCAGTCAC 74 GGGGAGAGC CTCCACCTC NFKBIE CTCGCTCACC 75 CTCATGAATC 76 TACACCCTGT ACTGCCAGGT IKB ACGAGCAGAT 77 CTTCCATGGT 78 alpha GGTCAAGGAG CAGTGCCTTT A20 CCTTGGAAGC 79 TTGTGTGGTT 80 ACCATGTTTG CGAGGCACAT CCL2 TGCCCCAGTC 81 CCCACTTCTGC 82 ACCTGCTGTT TTGGGGTCAGC IL6 GAAAGCAGCA 83 TTTCACCAGG 84 AAGAGGCACT CAAGTCTCCT RELA CCACGAGCTT 85 CTGGATGCGC 86 GTAGGAAAGG TGACTGATAG JUNB AAATGGAAC 87 TGTAGAGAG 88 AGCCCTTCT AGGCCACCA MCL1 GAGACCTTA 89 TTTGATGTC 90 CGACGGGTT CAGTTTCCG EGR1 AGCCCTACGA 91 AGCGGCCAGT 92 GCACCTGAC ATAGGTGATG KLF4 TCCCATCTTT 93 AGTCGCTTCA 94 CTCCACGTTC TGTGGGAGAG BCL6 CTGCAGATGG 95 TCTTCACGAG 96 AGCATGTTGT GAGGCTTGAT BCL3 CCTCTGGTGA 97 TACCCTGCAC 98 ACCTGCCTAC CACAGCAATA BCL-X GGTATTGGTG 99 TGCTGCATTG 100 AGTCGGATCG TTCCCATAGA E- CCTGGGACTC 101 TGTGAGCAAT 102 cadherin CACCTACAGA TCTGCTTGGA Desmo- GGCACCAGCA 103 ATCAAGCAGT 104 plakin GGATGTACT CGGAGCAGTT Vimentin TCAGAGAGAG 105 ATTCCACTTT 106 GAAGCCGAAA GCGTTCAAGG Cadherin- CAACGGACTAT 107 GAAAGGGCCA 108 11 GAAACACAGGA TTGCTGATAA Slug TCGGACCCAC 109 TGACCTGTCT 110 ACATTACCTT GCAAATGCTC Cyclin AGAGGCGGAG 111 GGCGGATTGG 112 D1 GAGAACAAAC AAATGAACTT Survivin GGACCACCGC 113 GTCTGGCTCG 114 ATCTCTACAT TTCTCAGTGG BCL2 GCCCTGTGGA 115 AGGGCCAAAC 116 TGACTGAGTA TGAGCAGAG ATF4 CCAACAACAG 117 GTGTCATCCA 118 CAAGGAGGAT ACGTGGTCAG BIP CACAGTGGTG 119 CAGTCAGATCAA 120 CCTACCAAGA AATGTACCCAG Hsp90B1 AACGGGCAAG 121 CGTCGAAGCA 122 GACATCTCTA TGTCTCTGAT DNAJC3 CATCTTGAATT 123 AGCCCTCCGA 124 GGGCAAGAAA TAATAAGCAA HERP GCGACTTGGA 125 CCAACAACAGC 126 GCTGAGTGG TTCCCAGAAT Erp72 AGCAGGTTTG 127 TTCTCTGACC 128 ATGTGAGTGG TTGGCAACAA EDEM1 GTGAAAGCCC 129 AGGCCACTCT 130 TTTGGAACCT GCTTTCCAAC Spliced CTGAGTCCG 131 ACTGGGTCCA 132 XBP1 CAGCAGGTG AGTTGTCCAG ERdj4 TTTCACAAGT 133 AAGCACTGTGAT 134 TGGCCATGAA CCAAGTGTATC SEC61A1 AGCAGCAGAT 135 CCTAGGAAGT 136 GGTGATGAGA CAGCCAGGAC gp130 GTCACCTCACA 137 TTTGAACAGGT 138 (human) CTCCTCCAAG CCAATGATTTC gp130 GGCACCAGCA 139 ATCAAGCAGT 140 (mouse) GGATGTACT CGGAGCAGTT Table legend: Abbreviations (for genes not dis- closed elsewhere): ″SOCS3″: suppressor of cyto- kine signaling 3; ″BIRC3″: baculoviral IAP re- peat containing 3; ″NFKB2″: Nuclear factor NF- kappa-B p100 subunit; ″NFKBIE″: Nuclear factor of kappa light polypeptide gene enhancer in B- cells inhibitor, epsilon; ″IKB alpha″: I-kappa- B-alpha; ″CCL2″: (C-C motif) ligand 2; ″IL6″: interleukin-6; ″BCL3″: B-cell CLL/lymphoma 3; ″BIP″: Binding immunoglobulin protein; ″Hsp90B1″: Heat shock protein 90kDa beta member 1; ″DNAJC3″: Endoplasmic reticulum DNA J domain-containing protein 6; ″HERP″: Drosophila melanogaster Homocysteine- induced endoplasmic reticulum protein; ″ERP″: endoplasmic reticulum protein 72; ″EDEM1″: ER degradation enhancer, mannosidase alpha-like 1; ″XBP1″: X-box binding protein 1; ″ERdj4″: DnaJ (Hsp40) homolog, subfamily B, member 9; ″SEC61A1″; Sec61 alpha 1 subunit; ″gp130″: glycoprotein 130.

Gene expression was analyzed in triplicate, normalized by 18S rRNA, and expressed as mean±SEM. For gene expression microarrays, RNA was isolated by Trizol, purified further on RNeasy columns, and profiled using Affymetrix Human Gene 1.0 ST arrays (Affymetrix). Results were deposited under GEO Accession: GSE46575.

Western Blotting, Immunoprecipitation, and Antibodies

Western blotting was performed as previously described (Battle T E, Arbiser J, & Frank D A (2005) The natural product honokiol induces caspase dependent apoptosis in B-cell chronic lymphocytic leukemia (B-CLL) cells. Blood 106(2):690-697). Antibodies to phospho-MAPK (9101), total MAPK (9102), phospho-Y705 STAT3 (9131), phospho-S6 (2215), total S6 (2217), phospho-4E-BP1 (9451), total 4E-BP1 (9644), total RSK (9355), phospho-S6K (9234, 85 used at 1:5000), total S6K (2708), phospho-eIF2α (9721, used at 1:1000), total eIF2α (5324), ATF4 (11815, used at 1:1000), PDGFRβ (3169), IGF1Rβ (9750), EGFR (2232), and HER2 (2242) were from Cell Signaling Technology. Phospho-RSK antibody was from R&D (AF889). Antibodies to total STAT3 (sc-482) and gp130 (sc-656, used at 1:1000) were from Santa Cruz Biotechnology. Phospho-S727 STAT3 antibody was described previously (229). REDD1 antibody was from Proteintech (10638-1-AP, used at 1:1000). Antibody recognizing full-length and cleaved ATF6 was from Abcam (ab122897, used at 1:1000). Antibodies to tubulin (T5168) and beta actin (A5316) were from Sigma. All antibodies were used at 1:10000 dilution for western blot unless otherwise noted. For immunoprecipitations, cells were lysed in 500 μl lysis buffer (0.5% NP-40, 150 mM NaCl, 50 mM Tris pH 7.5, with protease and phosphatase inhibitors freshly added at 1:100 [Pierce, PI78443]) on ice for 15 minutes, then centrifuged for 10 minutes at 14,000RPM and 4° C. The supernatant was transferred to a new tube and incubated with 10 μl JAK2 antibody (Santa Cruz sc-278) or a mix of two TYK2 antibodies, 10 μl of each (Santa Cruz sc-5271 and Cell Signaling Technology 9312). Immunoprecipitation was performed overnight at 4° C. with rotation. The next day, 75 μl of protein A/G beads (Santa Cruz sc-2003) were washed twice in lysis buffer, then incubated with immunoprecipitates overnight as before. The next day, the beads were spun down (1 min. at 7,500RPM and 4° C.) and washed 3 times with 650 μl lysis buffer for 10 minutes at 4° C. with rotation, then boiled in 50 μl sample buffer+10% β-mercaptoethanol. For Western blot, 20 μl were loaded per lane. For detection of phospho-tyrosine, a mixture of two pan-phospho-tyrosine antibodies (Cell Signaling Technology 9411 and 9416, 1:1000 of each) was used. Antibody to phospho-Y1007/1008 JAK2 was from Cell Signaling 86 Technology (3771, used at 1:1000). Antibody to phospho-Y570 JAK2 was from Millipore (09-241, used at 1:1000). Luminometric Assays Luciferase reporter cell lines were described previously (186). Firefly luciferase values were normalized by concurrent cell viability. Cell viability was measured as ATP-dependent luminescence by Cell Titer Glo (Promega).

Drug Treatments

For drug treatments, cells were spun down and suspended in fresh media the day prior. Atovaquone (Sigma-Aldrich, A7986) was dissolved at a stock concentration of 12.5 mM and used to treat cells at up to 1:500 dilution (up to 0.2% v/v DMSO final). JAK inhibitor 1 (Millipore 420097) was used at 1 μM, unless indicated otherwise. DTT (Bio-Rad 1610610) was dissolved at 1 M in PBS and used at 1:200 (5 mM final). Tunicamycin (Sigma-Aldrich T7765) was used at 5 μg/ml. Thapsigargin (T9033) was used at 1 μM. Brefeldin A (Millipore 203729) was used at 3 μg/ml. Rapamycin (Millipore 553210) was used at 10-100 μM as indicated. DMSO was used to dissolve all drugs unless otherwise specified.

Flow Cytometry

Annexin V/PI staining was performed using Annexin V:FITC Apoptosis Detection Kit I (BD Biosciences). Staining for cell cycle analysis was performed as previously described (267). Staining for cell-surface receptors was performed in 50 μl PBS+2% FBS with 2 μl antibody to IL6R (BioLegend #352803) or 5 μl antibody to gp130 (BD Biosciences #555757) for 20 minutes on ice in the dark. Cells were washed twice, then resuspended in 300 μl of the same buffer. Samples were analyzed on a BD FACSCanto II machine. Transfection and siRNA Cells were reverse-transfected using Lipofectamine RNAiMAX (Invitrogen); the culture medium was changed 24 hours later. Control siRNA (D-001210-02) and REDD1 siRNA (M-010855-01) were from Thermo Scientific Dharmacon.

Chart Review

Atovaquone start and end dates for approximately 500 AML patients who underwent HSCT at Dana-Farber Cancer Institute from 2006-2012 were obtained by chart review of the electronic medical record with DFCI IRB approval. Atovaquone was administered as a suspension, 750 mg twice daily. Due to the intermittent atovaquone dosing for some patients, a discontinuation for longer than 50 days disqualified subsequent atovaquone treatment from counting toward a patient's total atovaquone exposure. Patients who received more than one HSCT were excluded (4% of total patients).

Example 2 Identification of Atovaquone as a STAT3 Inhibitor

This example describes identification of atovaquone as a STAT3 inhibitor using a Connectivity Map.

Using a 12-gene signature of STAT3 activation, the Connectivity Map was queried to discover compounds that elicit gene expression changes contrary to the STAT3 signature (FIG. 1). The compound most opposed to the STAT3 signature was atovaquone (FIG. 2). In addition to being the leading hit, atovaquone was attractive for several other reasons. Most importantly, it is already FDA-approved, greatly reducing the cost and latency of bench-to bedside translation. Atovaquone, which is used clinically for infections caused by Pneumocystis, Toxoplasma, and Plasmodium, inhibits parasitic mitochondrial respiration and is not known to have any effects on mammalian cells (see, Baggish A L & Hill D R (2002) Antiparasitic agent atovaquone. Antimicrobial agents and chemotherapy 46(5):1163-1173). Furthermore, its side effects are minimal, and high plasma concentrations (15-30 μg/ml; 40-80 μM) are readily and routinely achieved in patients (Baggish & Hill, supra). For all these reasons, further investigation was focused on atovaquone as a putative STAT3 inhibitor and anti-cancer drug.

To determine if atovaquone inhibits STAT3, it was tested in a cell-based reporter system of STAT3 transcriptional activity (Nelson E A, et al. (2008) Nifuroxazide inhibits survival of multiple myeloma cells by directly inhibiting STAT3. Blood 112(13):5095-5102). These cells lack basal STAT3 activation; upon IL-6 treatment, STAT3 becomes activated and drives transcription of a STAT3-dependent luciferase reporter gene. The STAT3-luc reporter cells were pre-treated with drug for 1 hour, then stimulated with IL-6 (10 ng/ml) for 5 hr. Activity of firefly luciferase was measured and normalized by cell viability (Cell Titer Glo). Pre-treatment of the cells with atovaquone caused a dose-dependent inhibition of luciferase induction by IL-6, indicating suppression of STAT3 transcriptional activity (FIG. 3). To determine if atovaquone inhibits STAT3 activity specifically over other transcription factors, it was tested in cell-based reporter systems for STAT1 and STAT5, two other STAT family members, and NF-κB, an unrelated transcription factor. While the activity of these other transcription factors was modestly affected at the higher doses of atovaquone, the effect on STAT3 activity was much greater, indicating specificity for inhibition of STAT3 (FIG. 4). These results demonstrate atovaquone to be a novel STAT3 inhibitor.

Example 3 Mechanisms of Action of Atovaquone

This example demonstrates that atovaquone inhibits STAT3 phosphorylation, expression of endogenous STAT3 target genes, and viability of STAT3-dependent cancer cells.

The mechanism by which atovaquone inhibits STAT3 was investigated. STAT3-luc reporter cells were pre-treated with atovaquone (20 μM) for 1 hr, and then stimulated with IL-6 (10 ng/ml) for 15 minutes, 30 minutes, 1 hours, or 2 hours. Since STAT3 transcriptional activity is critically dependent on tyrosine phosphorylation, Western blotting was performed to see if atovaquone affected STAT3 phosphorylation. In the STAT3 reporter cells, atovaquone pre-treatment reduced STAT3 tyrosine phosphorylation following IL-6 stimulation (FIG. 5). A similar effect was observed in mouse embryonic fibroblasts (MEF), which were pre-treated with atovaquone (25 μM) for 30 minutes up to four hours, then stimulated with IL-6 (5 ng/ml) and soluble IL-6 receptor (20 μg/ml) for 15 minutes (FIG. 6). Next, atovaquone was used to treat U266 (2.5 hours), HEL (6 hours), or INA-6 cells (4 hours). Atovaquone inhibited constitutive STAT3 tyrosine phosphorylation in multiple cancer cell lines, while STAT3 serine phosphorylation, which is not critical to transcriptional activity, was not affected (FIG. 7). In U266 and INA-6 cells, the source of STAT3 activation is JAK-dependent IL-6 signaling, while in HEL cells, STAT3 is activated by mutant JAK2-V617F. Given that atovaquone inhibits constitutive STAT3 activation in cancer cells, it was asked whether atovaquone inhibits expression of endogenous STAT3 target genes in this context. In U266, INA-6 and HEL cells treated with atovaquone for 6 hours, expression of multiple STAT3 target genes was substantially downregulated (FIG. 8 and FIG. 9).

Next, the effect of atovaquone on the growth and survival of STAT3-dependent cancer cells was examined Survival of the multiple myeloma cell line INA-6 is exquisitely dependent on IL-6 added to culture medium and resultant STAT3 activation. Atovaquone suppressed the viability of INA-6 cells with an IC₅₀ of 11.9 μM, with complete loss of viability at higher doses (FIG. 10). The other cell lines with constitutively-active STAT3, U266 and HEL, were also killed by atovaquone. By contrast, the viability of non-malignant peripheral blood mononuclear cells (PBMC) was relatively preserved. To ascertain how atovaquone treatment reduced the viability of STAT3-dependent cancer cells, annexin V and PI staining followed by flow cytometry was performed on INA-6 cells treated with atovaquone (15 μM) for 24 hours and on U266 and HEL cells treated with atovaquone (20 μM) for 48 hours. These experiments revealed that atovaquone was inducing apoptotic cell death (FIG. 11 and FIG. 12).

Additionally, it was hypothesized atovaquone inhibits proliferation by disrupting cell cycle progression. An analysis of cell cycle distribution showed that atovaquone decreased the population of cells in G2/M and increased the proportion of cells with lower DNA content in HEL cells treated with atovaquone (25 μM) for 24 hours (FIG. 13). In summary, atovaquone inhibits constitutive STAT3 activation and target gene expression in cancer cells, and reduces their survival and proliferation.

Example 4 Atovaquone Selectively Inhibits Gp130 Cell-Surface Expression

This example demonstrates that atovaquone rapidly induces specific loss of cell-surface gp130, while total gp130 declines secondarily due to protein degradation.

To understand how atovaquone inhibits STAT3 phosphorylation, the possibility that atovaquone decreases the kinase activity of JAKs, which are responsible for STAT3 activation in the systems previously tested was considered. To assess kinase activity, the extent of kinase auto-phosphorylation, which provides a cellular readout of kinase activity, was first analyzed. Atovaquone treatment inhibited the auto-phosphorylation of JAK family members, showing that it diminished JAK kinase activity in cells (FIG. 14A-B). In particular, U266 cells were treated with atovaquone (15 μM) or JAK inhibitor 1(1 μM) for 1 hour, followed by lysis and immunoprecipitation to TYK2. The blot was probed with a pan-phospho-tyrosine antibody (FIG. 14A). Due to technical limitations, tyrosine phosphorylation of other JAK family members was not detected in U266 cells. Next, HEL cells were treated with atovaquone (20 μM) or JAK inhibitor 1 (1 μM) for 6 hours, followed by lysis and immunoprecipitation to JAK2, which was selected because these cells harbor mutant JAK2-V617F. The blot was probed with a pan-phospho-tyrosine antibody, as well as antibodies specific to phospho-Tyr570 and phospho-Tyr1007/1008 (FIG. 14B). Phospho-Tyr570 was previously reported to correlate better with kinase activity, whereas phospho-Tyr1007/1008 is paradoxically induced by certain JAK inhibitors, including JAK inhibitor 1, depending on binding mode In vitro kinase assays of atovaquone with JAK family members showed no inhibition (FIG. 15), ruling out the possibility that atovaquone was a direct JAK inhibitor. Therefore, it was hypothesized that atovaquone inhibits JAKs indirectly by acting on an upstream signaling component required for JAK activity. As receptor-associated kinases, JAK signaling depends upon direct interaction with plasma membrane-localized proteins for scaffolding. This requirement also extends to mutant JAK2-V617F. In particular, JAKs are frequently associated with gp130, a transmembrane protein that participates in the signaling of several cytokines, including IL-6, oncostatin M (OSM), and leukemia inhibitory factor (LIF). By contrast, gp130 is not involved in the signaling of prolactin or IFN-γ, which were used to activate STAT5 and STAT1 in their respective luciferase reporter systems. For these reasons, it was hypothesized that atovaquone inhibits the function or expression of gp130.

Flow cytometry was performed to measure the cell-surface expression of gp130 on U266 cells treated with atovaquone (20 μM), JAK inhibitor 1 (1 μM), or brefeldin A (3 μg/ml) for 2.5 hours, in which STAT3 phosphorylation was strongly suppressed by atovaquone. Interestingly, atovaquone substantially downregulated the cell-surface expression of gp130 but not IL-6 receptor (FIG. 16). A pharmacological JAK inhibitor did not affect gp130 expression, indicating this effect was not secondary to inhibition of STAT3 phosphorylation. Lastly, brefeldin A, which inhibits transport of proteins from ER to Golgi, reduced the cell surface expression of both gp130 and IL-6 receptor. Consequently, only atovaquone specifically inhibited the cell-surface expression of gp130. Atovaquone also induced downregulation of cell surface gp130 in INA-6 and HEL cells (FIG. 17).

Since atovaquone reduced gp130 expression at the cell surface, it was asked whether this effect was accompanied by reduced total gp130 in the cell. To address this question, a time course of atovaquone treatment was performed and total cellular gp130 was measured by Western blotting in U266 cells treated with atovaquone at 20 μM. STAT3 phosphorylation was inhibited rapidly, after only 10 minutes, whereas total gp130 was not reduced except at much longer time points (FIG. 18). Thus, it was surmised that atovaquone also rapidly downregulates cell-surface gp130, paralleling STAT3 inhibition and preceding the decrease in total gp130. This was confirmed by a flow cytometric time course experiment that demonstrated atovaquone rapidly inhibits the cell-surface expression of gp130, without affecting total gp130 until much later (FIG. 19). Loss of cell-surface gp130 may be due to decreased entry into the plasma membrane or increased internalization. In either case, the decrease in total gp130 observed at longer time points is likely due to degradation of relatively unstable intracellular gp130.

MEF, MDA-MB-468, and SKBR3 cells were treated with atovaquone (25 μM) for 6 or 12 hours, then analyzed by Western blot for expression of gp130 and various other receptors. It was found that atovaquone also induced loss of total gp130 after prolonged treatment in multiple other cell lines, including MEF, SKBR3, and MDA-MB-468 cells (FIG. 20). In contrast, levels of other receptors—such as PDGFR-β, EGFR, HER2, and IGF1R-β—were not affected, again indicating a specific effect on gp130. Also, gp130 mRNA expression was not significantly changed by atovaquone, demonstrating that the decrease in total gp130 occurs post-transcriptionally (FIG. 21). In summary, atovaquone rapidly induces specific loss of cell-surface gp130, while total gp130 declines secondarily due to protein degradation.

Example 5 Atovaquone Inhibits mTOR Activity Through REDD1

This example demonstrates that atovaquone inhibits the mTOR pathway by inducing the expression of REDD1.

Having characterized the effect of atovaquone on STAT3 and STAT3-dependent cell lines, it was asked if atovaquone had effects on the viability of cells that do not display constitutive STAT3 activation. K562 and AML2 cells treated with atovaquone (20 and 15 μM, respectively) for 48 hours. Interestingly, atovaquone also reduced the viability of various malignant hematological cell lines that lack STAT3 activation (FIG. 22 and FIG. 23). Similar to cells with activated STAT3, the loss of viability occurred through apoptosis and cell cycle arrest (FIG. 24 and FIG. 25). Therefore, it was hypothesized that atovaquone kills cancer cells through STAT3-related and STAT3-independent mechanisms. Accordingly, the hypothesis that atovaquone inhibited another common pathway in cancer pathogenesis was considered. In particular, the mTOR pathway, which is known to be involved in cancer cell growth and survival, was investigated.

K562 cells were treated with atovaquone (20 μM) or rapamycin (10 nM) for 1 hour or 5 hours, then analyzed by Western blot. In K562 cells lacking STAT3 activation, atovaquone inhibited phosphorylation of 4E-BP1, a direct mTOR substrate, and ribosomal protein S6 with efficacy comparable to rapamycin, but only after 5 hours of treatment (FIG. 26). Additionally, atovaquone inhibited phosphorylation of p70S6K, but not p42/44 MAPK, p90RSK, or Akt in K562 cells treated with atovaquone for 6 hours (FIG. 27). Taken together, these findings suggested that inhibition of the mTOR pathway by atovaquone was taking place at the level of mTOR itself. The requirement for prolonged treatment to observe mTOR inhibition raised the possibility that this effect was mediated by an induced factor. To test this hypothesis, cells were pretreated with cycloheximide, a protein synthesis inhibitor. K562 cells were pre-treated with vehicle or cycloheximide (2 μg/ml) for 1 hour, then treated with vehicle or atovaquone (20 μM) for 5 hours. Atovaquone inhibition of S6 phosphorylation in K562 and U266 cells was blocked in the presence of cycloheximide (FIG. 28 and FIG. 29). In contrast, cycloheximide did not affect the inhibition of STAT3 phosphorylation by atovaquone in U266 cells (FIG. 29), consistent with the rapid kinetics of this effect (FIG. 18). Similar results were obtained with actinomycin D, an inhibitor of mRNA synthesis. These results demonstrate that atovaquone inhibition of mTOR, but not STAT3, requires de novo gene expression.

To discover the gene whose induction by atovaquone was responsible for mTOR inhibition, gene expression microarrays were performed in K562 and U266 cells. It was reasoned that induction of the causative factor must be common to all cell lines in which atovaquone inhibits the mTOR pathway. Using a 1.5-fold cutoff, atovaquone upregulated several hundred genes in each cell line; however, only 19 of these genes were upregulated in both K562 and U266 cells. The expression of the 19 genes was then analyzed by qRT-PCR in additional cell lines responsive to atovaquone, resulting in the identification of a set of 4 genes that was consistently induced in all cell lines (FIG. 30). Of these, REDD1 is a known negative regulator of mTOR, whose activity is dependent on the TSC1/2-complex.

To evaluate the role of REDD1, RNA interference was used to knock down its expression in adherent SKBR3 cells, given the relative ease of introducing siRNA into these cells. SKBR3 cells were transfected with control or REDD1 siRNA for 48 hours, then treated with atovaquone (25 μM) for 4 hours. Knocking down REDD1 largely blocked atovaquone inhibition of S6 phosphorylation (FIG. 31). Moreover, atovaquone had no effect on S6 phosphorylation in MEFs with knockout of TSC2 or REDD1 itself following treatment with atovaquone (25 μM) for 2.5 hours (FIG. 32 and FIG. 33). Thus, atovaquone inhibits the mTOR pathway by inducing the expression of REDD1.

Example 6 Atovaquone Selectively Activates the Phospho-eIF2α/ATF4 Branch of the Unfolded Protein Response (UPR)

This example demonstrates that atovaquone inhibition of STAT3 is not secondary to UPR activation.

In asking how atovaquone induces REDD1, a possible role for ATF4, which regulates REDD1 expression was considered. ATF4 is regulated mainly at the level of translation and is induced upon phosphorylation of eIF2α. Moreover, in the set of genes consistently induced by atovaquone, ATF3 and CHOP are also ATF4 target genes, and CHAC1 is a target gene of CHOP. Growth-inhibitory and pro-apoptotic functions have been reported for all of these proteins, suggesting they may contribute to the anti-cancer activity of atovaquone. K562 and AML2 cells, which lack STAT3 activation, were treated with rapamycin for 72 hours. Indeed, rapamycin treatment of cancer cells lacking STAT3 activation caused only a modest decrease in viability, indicating that mTOR inhibition alone is not sufficient to fully explain the effects of atovaquone on viability of these cells (FIG. 34). For these reasons, it was hypothesized that atovaquone induces eIF2α phosphorylation, with a resulting increase in ATF4 protein and signaling. U266, K562, and SKBR3 cells were treated with atovaquone (20, 20, 25 μM respectively). It was found that atovaquone induced eIF2α phosphorylation and increased ATF4 protein levels in multiple cell lines, including U266, K562, and SKBR3 (FIG. 35 and FIG. 36). While ATF4 target genes were induced, expression of ATF4 mRNA was unchanged (FIG. 37), demonstrating that the increase in ATF4 protein occurred at the post-transcriptional level. The phospho-eIF2α/ATF4 pathway represents one branch of the UPR, whose other branches consist of ATF6 cleavage and IRE1-mediated XBP1 splicing. Interestingly, however, atovaquone did not induce spliced XBP1 (FIG. 38) or ATF6 cleavage (FIG. 39). Furthermore, in contrast to the UPR activators tunicamycin and thapsigargin, atovaquone did not induce any UPR target genes other than those downstream of ATF4 (FIG. 40). Thus, atovaquone selectively activates the phospho-eIF2α/ATF4 branch of the UPR. Since the UPR has been reported to inhibit IL-6-dependent STAT3 activation, various UPR activators (Tunicamycin, Thapsigargin, and Brefeldin A) were tested to determine if they also inhibit STAT3 phosphorylation in U266 cells. However, only brefeldin A decreased STAT3 phosphorylation (FIG. 41), consistent with its direct effects on cell-surface gp130 and IL-6 receptor. Consequently, atovaquone inhibition of STAT3 is not secondary to UPR activation.

Example 7 Atovaquone Treatment Associates with Improved Cancer Outcomes in Patients

This example demonstrates that atovaquone exerts anti-cancer effects in patients.

Atovaquone (trade name Mepron) is used clinically to protect hematological cancer patients against Pneumocystis pneumonia during treatment and after hematopoietic stem cell transplant (HSCT). At many transplant centers, patients receive atovaquone for 20-30 days upon discharge after HSCT, and then are switched to trimethoprim-sulfamethoxazole (TMPSMX; trade name Bactrim) for long-term prophylaxis. However, about 25% of patients are maintained on atovaquone for months or even years due to intolerance of TMP-SMX. In patients taking standard doses of atovaquone, plasma concentrations of 40-80 μM are routinely achieved (235), well within the range needed to inhibit STAT3 and mTOR in vitro. Consequently, retrospective analysis of atovaquone exposure and clinical outcomes after HSCT provides a unique opportunity to investigate the anti-cancer effects of atovaquone in patients. Acute myeloid leukemia (AML) was investigated based on the in vitro data showing the effects of atovaquone in AML cell lines, frequent STAT3 activation in AML patient samples (Schardt J A, et al. (2009) Activation of the unfolded protein response is associated with favorable prognosis in acute myeloid leukemia. Clinical cancer research: an official journal of the American Association for Cancer Research 15(11):3834-3841), association of UPR with better prognosis in AML (Schardt et al. supra), and sufficient sample size.

The patient population consisted of AML patients treated with HSCT at the Dana-Farber Cancer Institute and who survived at least 150 days after transplant without relapse. Patients treated with atovaquone for at least 100 days within the 150-day period were classified as “high atovaquone” exposure, while the remaining patients were classified as “low atovaquone” exposure. Importantly, patients in the “high atovaquone” group had significantly improved relapse-free survival, with a trend toward improved overall survival (FIG. 42). To further investigate the anti-cancer activity of atovaquone in patients, serum samples were collected from patients approximately 100 days following HSCT who were being treated with either TMP-SMX or atovaquone. The serum from the atovaquone-treated patients reduced the viability of U266 cells compared to the serum of patients receiving TMP-SMX (FIG. 43). Atovaquone is a colored compound, and its presence in patient plasma is visibly noticeable. Taken together, these results demonstrate that atovaquone exerts anti-cancer effects in patients.

Example 8 Buparvaquone and Sigma Analog Inhibit STAT-3-Dependent Gene Expression and STAT-3 and S6 Phosphorylation

This example demonstrates that the atovaquone analogs, buparvaquone and TDBHN (2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydroxy-1,4-naphthoquinone) (an analog available from Sigma-Aldrich), inhibit STAT3-dependent reporter gene expression, STAT3 phosphorylation and S6 phosphorylation.

STAT3-luc reporter cells were pre-treated with atovaquone, buparvaquone or TDBHN (concentration 10, 20, 30, or 40 μM) for 1 hour, then stimulated with IL-6 (10 ng/ml) for 5 hours. The activity of firefly luciferase was measured and normalized by cell viability (Cell Titer Glo). As shown in FIG. 44, all three compounds inhibited STAT-3 reporter gene expression relative to the controls.

Next, U266 cells were treated with 12.5 or 25 μM buparvaquone or 1, 5, or 25 μM 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydroxy-1,4-naphthoquinone (Sigma analog), or DMSO vehicle control, for 2.5 hours, after which cells were harvested and immunoblots were performed with antibodies for total and phospho STAT3 and total and phospho S6. As shown in FIG. 45, buparvaquone and the Sigma analog inhibited STAT3 and S6 phosphorylation at all concentrations tested, relative to vehicle control.

Example 9 Effect of Treatment with Atovaquone in an In Vivo Tumor Model

This Example demonstrates that atovaquone treatment reduced tumor growth rate and increased median survival times in a murine model of multiple myeloma.

To determine whether atovaquone displayed anti-cancer activity in animal models, we utilized xenografts of U266 human multiple myeloma cells (obtained from American Type Culture Collection (ATCC), Manassas, Va.), which display constitutive activation of both STAT3 and mTOR. Female NSG mice (obtained from The Jackson Laboratory, Bar Harbor, Me.) were injected subcutaneously with 5×10⁶ U266 cells in 30% Matrigel, and tumors were allowed to grow to a volume of approximately 100 mm³ At that point, animals were treated daily by oral gavage with either vehicle (5% benzyl alcohol in water), generic atovaquone, or Mepron® brand atovaquone (GlaxoSmithKline LLC, Philadelphia, Pa.) at a dose of 200 mg/kg. Treatment with either form of atovaquone led to a prominent decrease in the growth rate of these tumors (FIG. 46A) as well as an increase in the median survival of the treated animals (FIG. 46B).

Discussion

Upon determining that atovaquone decreased the viability of malignant hematological cell lines, including cells that lacked STAT3 activation, a systematic approach was taken to determine the effects of atovaquone on other intracellular signaling pathways that mediated malignant cell behavior. From these studies, it was found that atovaquone inhibited the mTOR pathway. While it was as efficacious as rapamycin in inhibiting this pathway, the fact that atovaquone required several hours of exposure to inhibit this pathway, and lost activity when cells were treated with a protein synthesis inhibitor, suggested that it was operating by a unique mechanism that required new protein synthesis. Subsequent experimentation revealed that atovaquone induced the phospho-eIF2α/ATF4 pathway and REDD1 expression, which is necessary for atovaquone-induced mTOR inhibition. While not intending to be bound by any one particular theory or mechanism of action, it is believed that this unique manner in which atovaquone is thought to inhibit the mTOR pathway and exert an anti-cancer effect is superior to that of the mTOR inhibitor rapamycin.

It has been discovered, using an unbiased gene expression-based approach, that atovaquone is a novel STAT3 inhibitor. Atovaquone acts by diminishing cell-surface gp130 expression and STAT3 tyrosine phosphorylation. As a consequence, critical STAT3 target genes mediating survival and proliferation are reduced, such as survivin, Bcl-2 family members, and cyclin D1. Moreover, atovaquone inhibits the viability of STAT3-dependent cancer cells by inducing apoptosis and disrupting cell cycle progression. Since atovaquone inhibits STAT3 signaling upstream of JAK kinases, its mechanism predicts that atovaquone will also inhibit phosphorylation of other STATs if they are activated alongside STAT3 by the same upstream events. Indeed, in addition to inhibiting STAT3 phosphorylation, atovaquone inhibited IL-6-dependent phosphorylation of STAT1 in INA-6 and U266 cells and mutant JAK2-dependent phosphorylation of STAT1 and STAT5 in HEL cells. Since STAT5 activation is crucial to cancer pathogenesis caused by JAK2-V617F, the additional inhibition of STAT5 in this context is a desirable effect of atovaquone. By contrast, atovaquone did not inhibit STAT5 phosphorylation in K562 cells, in which STAT5 is activated by BCR-ABL independent of gp130. Because the effects of atovaquone on STAT activation are restricted to gp130-dependent signaling, atovaquone inhibits STATs more selectively than direct pharmacological JAK inhibition. For example, signaling due to growth hormone, erythropoietin, and interferons is abrogated by JAK inhibitors but remains intact under atovaquone, since these hormones and cytokines do not utilize gp130. This reduces the potential side effects of atovaquone, which is already known to be extremely well-tolerated in humans. At the same time, the actions of atovaquone extend to all cytokines that signal through gp130, including LIF and OSM, thereby exerting broader effects than therapies specifically directed against IL-6 or IL-6 receptor, such as monoclonal antibodies. This is also advantageous, since oncogenic effects of LIF and OSM have been reported.

The present Examples demonstrate that IL-6-dependent STAT3 signaling, a key cancer pathway, is effectively inhibited by atovaquone. For example, IL-6 is a critical survival factor in AML and multiple myeloma, which is pertinent to the cell lines used in this study and the findings in AML patients. Moreover, the importance of IL-6 has been established in multiple solid malignancies, including breast, lung, and melanoma. Besides STAT3 activation due to IL-6, it was also demonstrates herein that atovaquone inhibits STAT activation due to mutant JAK2-V617F, which is crucial to myeloproliferative neoplasms. Thus, atovaquone can be used for the treatment of multiple diverse cancers, either as initial therapy or as a second-line option if JAK resistance mutations emerge following JAK inhibitor therapy. Atovaquone can also be combined with a JAK inhibitor to decrease the likelihood of developing resistance. In addition, the present Examples demonstrate that atovaquone activates the phospho-eIF2α/ATF4 branch of the UPR, resulting in induction of REDD1, which mediates mTOR inhibition, and induction of the pro-apoptotic factors CHOP and CHAC1 Inhibiting mTOR has intrinsic anticancer value due to its involvement in tumor cell survival and proliferation. However, recent studies also support specific benefits associated with dual blockade of the JAK/STAT and mTOR pathways, as shown in breast cancer and ALL. Moreover, mTOR is known to phosphorylate STAT3 on serine 727 and increase its transcriptional activity. Although this mode of crosstalk was not observed in this study, it illustrates how the various effects of atovaquone can complement and potentially synergize with one another. While broad UPR activation has variable effects in cancer, the EIF2α/ATF4 pathway has been shown to promote apoptosis in numerous cancer contexts. Additionally, the net effect of UPR activation appears to depend on the balance between induction of pro-survival BiP and pro-apoptotic CHOP. Atovaquone strongly upregulates CHOP with no effect on levels of BiP, supporting the role of the EIF2α/ATF4 pathway in atovaquone-mediated apoptosis. CHAC1, an EIF2α/ATF4 target gene consistently upregulated by atovaquone, is also pro-apoptotic. Thus, atovaquone inhibits the viability of cancer cells through STAT3-related and STAT3-independent mechanisms.

Therefore, in light of all the above findings, the use of atovaquone and related compounds in the treatment of cancer is strongly indicated. Moreover, the risk of side effects is not a great concern given the safe track record of atovaquone use in the clinic.

A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims. 

1. A method of decreasing the growth of a cancer cell, the method comprising delivering to a target cancer cell a growth-inhibitory amount of an atovaquone-related compound, wherein, prior to the delivery, an increased level of activation of the mammalian target of rapamycin (mTOR) pathway in the cancer compared to a control level of activation of the mTOR pathway has been found.
 2. The method of claim 1, wherein, prior to the delivery, an increased level of activation of the signal transducer and activator of transcription 3 (STAT3) pathway in the cancer compared to a control level of activation of the STAT3 pathway has been found.
 3. The method of claim 1, wherein the target cancer cell is in a mammalian subject or a human subject.
 4. (canceled)
 5. The method of claim 3, wherein the delivery comprises administration of the compound to the subject.
 6. The method of claim 1, wherein the level of activation of the mTOR pathway in the cancer was detected in a test sample of or from one or more test cells from the cancer and the control level of activation of the mTOR pathway was detected in a control sample of or from one or more control cells, or the level of activation of the mTOR pathway in the cancer was detected in microvesicles or exosomes obtained from a test sample of a body fluid of a subject with the cancer and the control level of activation of the mTOR pathway was detected in microvesicles or exosomes obtained from a control sample of the body fluid.
 7. (canceled)
 8. The method of claim 2, wherein the level of activation of the STAT3 pathway in the cancer was detected in a test sample of or from one or more test cells from the cancer and the control level of activation of the STAT3 pathway was detected in a control sample of or from one or more control cells, or the level of activation of the STAT3 pathway in the cancer was detected in microvesicles or exosomes obtained from a test sample of a body fluid of a subject with the cancer and the control level of activation of the STAT3 pathway was detected in microvesicles or exosomes obtained from a control sample of the body fluid.
 9. (canceled)
 10. The method of claim 6, wherein the body fluid is selected from the group consisting of blood, lymph, urine, cerebrospinal fluid (CSF), ascites, and pleural fluid.
 11. The method of claim 1, wherein the compound is selected from the group consisting of atovaquone, buparvaquone, and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone, or the compound is atovaquone and the growth-inhibitory amount of the atovaquone is in a range of about 10 to about 40 mg/kg per day. 12.-13. (canceled)
 14. A method of determining the susceptibility of a cancer in a subject to the growth-inhibitory effect of an atovaquone-related compound, the method comprising, assessing the level of activation of the mTOR pathway in a test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level activation of the mTOR pathway is not detected in the test sample compared to a control level of activation of the mTOR pathway than if an increased level of activation of the mTOR pathway is detected in the test sample compared to a control level of activation of the mTOR pathway.
 15. The method of claim 14, further comprising, assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject, identifying the cancer as likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the STAT3 is detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway, and identifying the cancer as less likely to be susceptible to the growth-inhibitory effect of the atovaquone-related compound if an increased level of activation of the STAT3 pathway is not detected in the test sample or the second test sample compared to a control level of activation of the STAT3 pathway than if an increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample compared to a control level of activation of the mTOR pathway.
 16. The method of claim 14, wherein the test sample is a sample of or from one or more cancer cells from the subject, or the test sample comprises microvesicles or exosomes obtained from a body fluid of the subject.
 17. (canceled)
 18. The method of claim 15, wherein the second test sample is a sample of or from one or more cancer cells from the subject, or the second test sample comprises microvesicles or exosomes obtained from a body fluid of the subject.
 19. (canceled)
 20. The method of claim 17, wherein the body fluid is selected from the group consisting of blood, lymph, urine, CSF, ascites, and pleural fluid.
 21. The method of claim 14, further comprising administering an atovaquone-related compound to the subject if the increased level activation of the mTOR pathway is detected in the test sample.
 22. The method of claim 15, further comprising administering an atovaquone-related compound to the subject if the increased level of activation of the mTOR pathway is detected in the test sample, if the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample, or if the increased level activation of the mTOR pathway is detected in the test sample and the increased level of activation of the STAT3 pathway is detected in the test sample or the second test sample.
 23. The method of claim 21, wherein the compound is selected from the group consisting of atovaquone, buparvaquone, and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone.
 24. (canceled)
 25. A method of assessing the success of cancer cell growth inhibitory therapy with an atovaquone-related compound in a subject, the method comprising, assessing the level of activation of the mTOR or eIF2α/ATF4 pathway in a test sample from a subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is lower than the level of activation of the mTOR pathway in a control sample, or if the level of activation of the eIF2α/ATF4 pathway in the test sample is lower than the level of activation of the eIF2α/ATF4 pathway in a control sample, and not identifying the treatment as having been successful if the level of activation of the mTOR pathway in the test sample is not lower than the level of activation of the mTOR pathway in a control sample and the level of activation of the eIF2α/ATF4 pathway in the test sample is not lower than the level of activation of the eIF2α/ATF4 pathway in a control sample.
 26. The method of claim 25, further comprising, assessing the level of activation of the STAT3 pathway in the test sample or a second test sample from the subject that has been treated with the compound, identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is lower than the level of activation of the STAT3 pathway in a control sample or a second control sample, and not identifying the treatment as having been successful if the level of activation of the STAT3 pathway in the test sample or the second test sample is not lower than the level of activation of the STAT3 pathway in the control sample or the second control sample.
 27. The method of claim 25, wherein the test sample is a sample of or from one or more cancer cells from the subject, or the test sample comprises microvesicles or exosomes obtained from a body fluid of the subject.
 28. (canceled)
 29. The method of claim 26, wherein the second test sample is a sample of or from one or more cancer cells from the subject, or the second sample comprises microvesicles or exosomes obtained from a body fluid of the subject.
 30. (canceled)
 31. The method of claim 25, wherein the control sample was obtained from the subject prior to the treatment with the atovaquone-related compound.
 32. The method of claim 31, wherein the control sample is a sample of or from one or more cancer cells from the subject, or the control sample comprises microvesicles or exosomes obtained from a body fluid of the subject.
 33. (canceled)
 34. The method of claim 27, wherein the body fluid is selected from the group consisting of blood, lymph, urine, CSF, ascites, and pleural fluid.
 35. The method of claim 25, wherein the subject is a mammalian subject or a human subject.
 36. (canceled)
 37. The method of claim 25, wherein the compound is selected from the group consisting of atovaquone, buparvaquone, and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone.
 38. (canceled)
 39. A method of treating cancer in a patient, the method comprising: administering a therapeutically effective amount of an atovaquone-related compound to a patient in need thereof; and, after the administration, monitoring the level of activation of the mTOR or eIF2α/ATF4 pathway in a test sample, two or more serial test samples, a second test sample, or a second set of two or more serial test samples from the patient.
 40. The method of claim 39, further comprising, after the administration, monitoring the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples from the patient.
 41. The method of claim 39, further comprising continuing the treatment if the level of activation of the mTOR pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment.
 42. The method of claim 40, further comprising continuing the treatment if the level of activation of the STAT3 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is decreased relative to its level of activation in a control sample obtained from the patient prior to treatment.
 43. The method of claim 39, wherein the test sample, each of the two or more serial test samples, the second test sample, or each of the second set of two or more serial test samples is a sample of or from one or more cancer cells from the subject, or the test sample, each of the two or more serial test samples, the second test sample, or each of the second set of two or more serial test samples comprises microvesicles or exosomes obtained from a body fluid of the subject. 44.-46. (canceled)
 47. The method of claim 43, wherein the body fluid is selected from the group consisting of blood, lymph, urine, CSF, ascites, and pleural fluid.
 48. The method of claim 39, wherein the patient is a mammalian subject or a human subject.
 49. (canceled)
 50. The method of claim 39, wherein the compound is selected from the group consisting of atovaquone, buparvaquone, and 2-(4-(trans-decahydronaphth-2-yl)butyl)-3-hydoxy-1,4-naphthoquinone, or the compound is atovaquone and the therapeutically effective amount of the atovaquone is in a range of about 10 to about 40 mg/kg per day. 51.-52. (canceled)
 53. The method of claim 39, further comprising administering an additional therapy to the patient.
 54. The method of claim 53, wherein the additional therapy is selected from the group consisting of chemotherapy, immunotherapy, targeted therapy, and/or radiation therapy.
 55. The method of claim 1, wherein the cancer is a hematological tumor selected from the group consisting of acute myeloid leukemia, chronic myeloid leukemia, Hodgkin lymphoma, non-Hodgkin lymphoma, multiple myeloma, acute lymphoblastic leukemia, and chronic lymphocytic leukemia, or the cancer is a solid tumor selected from the group consisting of breast cancer, endometrial cancer, melanoma, lung cancer, ovarian cancer, pancreatic cancer, colorectal cancer, prostate cancer, brain cancer, gastroesophageal cancer, kidney cancer, non-small cell lung, neuroendocrine cancer, and glioblastoma multiforme.
 56. (canceled)
 57. The method of claim 1, wherein the level of activation of the mTOR pathway is determined by detecting the level of phosphorylation of one or more polypeptides selected from the group consisting of mTOR, ribosomal protein S6, S6 kinase, 4E-BP1, and eIF2α.
 58. The method of claim 2, wherein the level of activation of the STAT3 pathway is determined by detecting the level of one or more of the following markers: STAT3 phosphorylation, nuclear localization of STAT3, STAT3 DNA binding, STAT3-dependent gene expression, and JAK family kinase autophosphorylation.
 59. The method of claim 58, wherein the STAT3 phosphorylation comprises phosphorylation of tyrosine 705 of human STAT3.
 60. The method of claim 58, wherein detecting STAT3-dependent gene expression comprises determining the expression level of one or more of STAT3 regulated genes encoding polypeptides selected from the group consisting of: myeloid cell leukemia sequence 1 (BCL2-related) (MCL1), jun B proto-oncogene (JUNB), B-cell CLL/lymphoma 6 (BCL6), nuclear factor, interleukin 3 regulated (NFIL3), calpain 2, (m/II) large subunit (CAPN2), early growth response 1 (EGR1), vascular endothelial growth factor A (VEGF), protein tyrosine phosphatase type IVA, member 1 (PTPCAAX1), Kruppel-like factor 4 (KLF4), exostosin glycosyltransferase 1 (EXT1), Niemann-Pick disease, type C1 (NPC1), p21 protein (Cdc42/Rac)-activated kinase 2 (PAK2), pericentrin (PCNT), fibrinogen-like 2 (FGL2), angiopoietin 1 (ANGPT1), GRB10 interacting GYF protein 1 (GIGYF1) (PERQ1), ceroid-lipofuscinosis, neuronal 6, late infantile, variant (CLN6), Brother of CDO (BOC), cysteine dioxygenase (CDO), BCL2-like 1 (BCL2L1) (BCLX), CYCLIN D1, SURVIVIN, and B-cell CLL/lymphoma 2 (BCL2).
 61. The method of claim 60, wherein the level of STAT3 pathway activation correlates with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides selected from the group consisting of MCL1, JUNB, BCL6, NFIL3, CAPN2, EGR1, VEGF, PTPCAAX1, KLF4, EXT1, NPC1, PAK2, BCLX, SURVIVIN, and BCL2.
 62. The method of claim 60, wherein the level of STAT3 pathway activation correlates inversely with the level of expression of one or more of the STAT3-regulated genes encoding polypeptides selected from the group consisting of PCNT, FGL2, ANGPT1, PERQ1, CLN6, BOC, and CDO.
 63. (canceled)
 64. The method of claim 25, further comprising determining the level of expression of one or more of CCAAT/-enhancer-binding protein homologous protein (CHOP), cation transport regulator-like 1 protein (CHAC1), and regulated in development and DNA damage responses-1 protein (REDD1). 65.-78. (canceled)
 79. The method of claim 39, further comprising determining the level of expression of one or more of CHOP, CHAC1, and REDD1. 80.-81. (canceled)
 82. The method of claim 39, further comprising continuing the treatment if the level of activation of the eIF2α/ATF4 pathway in the test sample, the two or more serial test samples, the second test sample, or the second set of two or more serial test samples is increased relative to its level of activation in a control sample obtained from the patient prior to treatment. 83.-98. (canceled) 